Isotachophoresis for purification of nucleic acids

ABSTRACT

The present disclosure relates to fluidic systems and devices for processing, extracting, or purifying one or more analytes. These systems and devices can be used for processing samples and extracting nucleic acids, for example by isotachophoresis. In particular, the systems and related methods can allow for extraction of nucleic acids, including non-crosslinked nucleic acids, from samples such as tissue or cells. The systems and devices can also be used for multiplex parallel sample processing.

CROSS-REFERENCE

This is a continuation application of PCT/US2017/015519, filed on Jan.28, 2017, entitled “Isotachophoresis for Purification of Nucleic Acids”[Attorney Docket No. 43647-712.601], which claims the benefit of U.S.Provisional Application No. 62/288,930, filed Jan. 29, 2016, entitled“Isotachophoresis for Purification of Nucleic Acids” [Attorney DocketNo. 43647-712.101], the entire contents of which are herein incorporatedby reference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with the support of the United States governmentunder contract number 1R43HG007620-01 awarded by the National Institutesof Health. The government has certain rights in the invention.

BACKGROUND

Formalin-fixed paraffin-embedded (FFPE) samples have been collected,prepared, stored, and archived in large tissue banks for more than acentury. As of 2008, there were over 400 million FFPE samples stored inbiobanks worldwide, and this number is growing. These samples are oftenaccompanied by clinical information such as primary diagnosis,therapeutic regimen, and follow-up data, making them an importantresource for the development of therapeutics and the discovery of genomeand transcriptome biomarkers.

Sample preparation methods to extract and purify nucleic acids from FFPEsamples remain manually intensive and laborious. Approaches for FFPEextraction and purification vary widely but often includedifficult-to-automate and difficult-to-accelerate steps of wax removal,centrifugation, buffer exchanges, temperature control, cross-linkreduction and enzyme treatment. FFPE generally refers to cross-linkingproteins in a sample using formalin and embedding the sample in paraffin(wax). FFPE treatment of a sample often enables the sample to bepreserved over time and can be especially useful for long-term storage.The cross-linked proteins may bind up the DNA and RNA in the sample,thereby generally making it unusable for downstream applications such asamplification, library preparation, or sequencing.

Removal of paraffin and protein crosslinks in FFPE samples may be achallenging process. Deparaffinization is traditionally performed usinghighly flammable xylenes. Alternately or in series, the sample can betreated with other solvents, mineral oil and alkaline chemistry and/orelevated temperature. After deparaffinization, proteins in the samplecan be treated with different agents or subjected to conditions that mayrequire additional time and effort.

At the end of digestion and denaturation, a mix of crosslinked andnon-crosslinked nucleic acids may remain. Removal of the non-crosslinkedmaterial may be important for high quality results from assays such asamplification or sequencing; in some cases, if the fraction ofnon-crosslinked material is too low, the downstream assay may fail toperform resulting in a loss of not only the sample itself, but alsolabor, time and resources.

SUMMARY

Isotachophoresis (ITP) is an electrophoretic technique which can use adiscontinuous buffer containing a leading electrolyte (LE) with a highereffective mobility magnitude and a trailing electrolyte (TE) with alower effective mobility magnitude (e.g., relative to the LE) to focussample species that have a greater effective mobility magnitude than thetrailing electrolyte but a lower effective mobility magnitude than theleading electrolyte. ITP can selectively focus nucleic acids fromsamples by more than 10,000-fold in less than five minutes. The presentdisclosure provides methods and devices employing and automating ITP forsample preparation, including extraction, purification, enrichment, andhighly sensitive quantitation, and is particularly useful for preparingand purifying nucleic acids from FFPE samples and other biologicalsamples.

Sample preparation is important to genomic analysis, yet it remains aprimary source of analysis variability and can require significantmanual labor. The present disclosure includes techniques and devices toaddress this challenge, such as by using on-chip isotachophoresis (ITP)for extraction and purification of nucleic acids. These techniquesinclude methods to enrich (concentrate) non-crosslinked nucleic acids toenable higher yield and higher quality nucleic acid sample preparationand produce more useable samples (e.g., fewer quality-check rejections)from FFPE and other preserved or fresh samples.

The present disclosure includes techniques and devices for automation ofnucleic acid sample preparation from samples, including solid tissue,lysed solid tissue, preserved or fixed tissue samples (e.g., FFPE),whole blood, plasma and serum, buccal swabs, dried blood spots and otherforensic samples, fresh or fresh frozen (FF) tissues, biopsy tissue,organ tissue, solid organ tissue, samples comprising connections (e.g.gap junctions, tight junctions, adherent junctions) between cells,cultured or harvested cells from blood or tissues, stool, and bodilyfluids (e.g., saliva, urine), or any combination thereof. Samples caninclude cellular and cell-free nucleic acids, for both eukaryotic andprokaryotic organisms, or any combination thereof. The techniques of thepresent disclosure, compared to existing approaches, can be faster, lessmanually intensive, more suited for both small and large startingamounts of tissue, and can achieve higher yield from samples and higherquality analyses of samples.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a fluidic device (i) a tissuesample comprising lysed solid tissue, wherein said lysed solid tissuecomprises nucleic acids and a contaminant, (ii) a trailing electrolytebuffer comprising first trailing electrolyte ions with an effectivemobility having a magnitude lower than a magnitude of an effectivemobility of said nucleic acids, and (iii) a leading electrolyte buffercomprising first leading electrolyte ions, with a second effectivemobility, wherein said second effective mobility has a magnitude greaterthan said magnitude of said effective mobility of said nucleic acids;and (b) applying an electric field within said fluidic device to conductisotachophoresis with said first trailing electrolyte ions, said nucleicacids, and said first leading electrolyte ions, thereby purifying saidnucleic acids from said contaminant in said tissue sample.

In some embodiments of aspects provided herein, said effective mobilityof said first trailing electrolyte ions has a magnitude greater than amagnitude of an effective mobility of said contaminant. In someembodiments of aspects provided herein, said fluidic device is amicrofluidic chip and said tissue sample, said trailing electrolytebuffer and said leading electrolyte buffer are loaded into a first zoneof said microfluidic chip. Some embodiments of aspects provided hereinmay further comprise, in said first zone of said microfluidic chip,conducting on said tissue sample at least one sample preparationprocedure selected from the group consisting of (1) removing embeddingmaterial, (2) disrupting tissue, (3) lysing cells, (4) de-crosslinkingsaid nucleic acids, (5) digesting proteins, and (6) digesting saidnucleic acids. In some embodiments of aspects provided herein, saidisotachophoresis is conducted in a second zone of said microfluidicchip, wherein said second zone is separate from and fluidicallyconnected to said first zone. In some embodiments of aspects providedherein, said solid tissue is derived from a solid organ. In someembodiments of aspects provided herein, said lysed solid tissuecomprises a chemical fixative. In some embodiments of aspects providedherein, said chemical fixative is formalin. In some embodiments ofaspects provided herein, said solid tissue is formalin fixed paraffinembedded tissue (FFPE). In some embodiments of aspects provided herein,said lysed solid tissue comprises urea or thiourea. Some embodiments ofaspects provided herein further comprise disrupting cell-cell junctions,extracellular matrix, or connective tissue in order to obtain said lysedsolid tissue. In some embodiments of aspects provided herein, said lysedsolid tissue comprises solid particles. In some embodiments of aspectsprovided herein, said nucleic acids comprise dispersed or solvatednucleic acids. In some embodiments of aspects provided herein, saidcontaminant is selected from the group consisting of crosslinked nucleicacids, embedding material, tissue debris, fixation chemicals, proteins,inhibitors, and combinations thereof. In some embodiments of aspectsprovided herein, said contaminant comprises crosslinked nucleic acids.In some embodiments of aspects provided herein, said tissue sample iscombined with said trailing electrolyte buffer prior to said loading. Insome embodiments of aspects provided herein, said tissue sample iscombined with said leading electrolyte buffer prior to said loading. Insome embodiments of aspects provided herein, said loading of saidleading electrolyte buffer is conducted prior to said loading of saidtissue sample. In some embodiments of aspects provided herein, saidsolid tissue is lysed in said leading electrolyte buffer prior to saidloading of said tissue sample. In some embodiments of aspects providedherein, said solid tissue is lysed in said trailing electrolyte bufferprior to said loading of said tissue sample. In some embodiments ofaspects provided herein, said sample preparation procedure comprises,prior to said applying of said electric field, removing embeddingmaterial by incubating said tissue sample in said fluidic device at atemperature of at least about 37° C. for a duration of at least about 1minute. In some embodiments of aspects provided herein, said temperatureis from about 40° C. to about 80° C. In some embodiments of aspectsprovided herein, said duration is from about 1 minute to about 120minutes. In some embodiments of aspects provided herein, said samplepreparation procedure comprises disrupting tissue or lysing cells byapplying mechanical stress to said tissue sample. In some embodiments ofaspects provided herein, said sample preparation procedure comprisesdisrupting tissue or lysing cells by applying heat to said tissuesample. In some embodiments of aspects provided herein, said applyingheat results in a temperature of said tissue sample from about 30° C. toabout 80° C. In some embodiments of aspects provided herein, said samplepreparation procedure comprises disrupting tissue or lysing cells bycontacting said tissue sample with a solution with pH of at least 10 orby proteolytically digesting said tissue sample. In some embodiments ofaspects provided herein, said proteolytic digestion is conducted at atemperature greater than about 25° C. In some embodiments of aspectsprovided herein, said sample preparation procedure comprises disruptingtissue or lysing cells by applying at least one surfactant to saidtissue sample. In some embodiments of aspects provided herein, saidsample preparation procedure comprises disrupting tissue or lysing cellsby applying a solution comprising urea to said tissue or cell sample. Insome embodiments of aspects provided herein, said solution furthercomprises thiourea. In some embodiments of aspects provided herein, aconcentration of said urea in said solution is within a range of fromabout 4 M to about 9 M and a concentration of said thiourea in saidsolution is in a range of from about 0.5 M to about 3.5 M. In someembodiments of aspects provided herein, a concentration of said urea insaid solution is from about 6.5 M to about 7.5 M and a concentration ofsaid thiourea in said solution is from about 1.5 M to about 2.5 M. Insome embodiments of aspects provided herein, said sample preparationprocedure comprises de-crosslinking said nucleic acids by digestingcrosslinking proteins with proteinase K. In some embodiments of aspectsprovided herein, said sample preparation procedure comprises digestingsaid nucleic acids with DNase or RNase. Some embodiments of aspectsprovided herein further comprise eluting an output solution comprisingsaid purified nucleic acids from an outlet reservoir of said fluidicdevice. In some embodiments of aspects provided herein, a concentrationof said purified nucleic acids in said output solution is at least abouttwo-fold higher than a concentration of said nucleic acids in saidtissue sample. In some embodiments of aspects provided herein, saidtissue sample and said purified nucleic acids in said output solutioncomprise crosslinked nucleic acids and a concentration of saidcrosslinked nucleic acids in said output solution is at least abouttwo-fold lower than a concentration of said crosslinked nucleic acids insaid tissue sample. In some embodiments of aspects provided herein, saidcontaminant is present in said output solution at a concentration thatis at least two-fold less than a concentration of said contaminant insaid tissue sample. In some embodiments of aspects provided herein, saidfirst trailing electrolyte ions comprise caproic acid. In someembodiments of aspects provided herein, said first leading electrolyteions comprise chloride. In some embodiments of aspects provided herein,said trailing electrolyte buffer comprises second trailing electrolyteions having a different effective mobility than said first trailingelectrolyte ions. In some embodiments of aspects provided herein, saidsecond trailing electrolyte ions comprise HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) or MOPS(3-(N-morpholino)propanesulfonic acid). In some embodiments of aspectsprovided herein, said second trailing electrolyte ions comprise HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) and said firsttrailing electrolyte ions comprise caproic acid. In some embodiments ofaspects provided herein, said second trailing electrolyte ions compriseMOPS (3-(N-morpholino)propanesulfonic acid) and said first trailingelectrolyte ions comprise caproic acid. In some embodiments of aspectsprovided herein, said second trailing electrolyte ions comprise HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) and said firsttrailing electrolyte ions comprise MOPS. In some embodiments of aspectsprovided herein, said trailing electrolyte buffer comprises secondtrailing electrolyte ions with a second effective mobility, wherein saidsecond effective mobility has a magnitude about the same as or lowerthan said magnitude of said effective mobility of said contaminant. Insome embodiments of aspects provided herein, said tissue sample loadedinto said fluidic device has a volume of at least 50 μl. Someembodiments of aspects provided herein further comprise, in said firstzone of said microfluidic chip, conducting on said tissue sample a firstsample processing procedure, and in a second zone of said microfluidicchip, conducting on said tissue sample an enzymatic reaction. In someembodiments of aspects provided herein, said first sample processingprocedure comprises removal of embedding material, disruption of tissue,or cell lysis, and said enzymatic reaction comprises de-crosslinkingsaid nucleic acids, digesting proteins, or digesting nucleic acids. Insome embodiments of aspects provided herein, said first zone and saidsecond zone each are each heated to a temperature above 37° C. In someembodiments of aspects provided herein, said first zone is heated to atemperature of about 60° C. to 100° C. during said first sampleprocessing procedure and wherein said second zone is heated to atemperature of 40° C. to 60° C.

An aspect of the present disclosure provides a method for simultaneouslypurifying nucleic acids from at least two different samples comprising:(a) loading into a first channel of a microfluidic chip (i) a firstsample comprising first nucleic acids and a first contaminant, (ii) afirst trailing electrolyte buffer comprising first trailing ions,wherein a magnitude of an effective mobility of said first trailing ionsis less than a magnitude of an effective mobility of said first nucleicacids, and (iii) a first leading electrolyte buffer comprising firstleading ions, wherein a magnitude of an effective mobility of said firstleading ions is greater than said magnitude of said effective mobilityof said first nucleic acids; (b) loading into a second channel of saidmicrofluidic chip (i) a second sample comprising second nucleic acidsand a second contaminant, (ii) a second trailing electrolyte buffercomprising second trailing ions, wherein a magnitude of said secondtrailing ions is less than a magnitude of an effective mobility of saidsecond nucleic acids, and (iii) a second leading electrolyte buffercomprising second leading ions, wherein a magnitude of an effectivemobility of said second leading ions is greater than said magnitude ofsaid effective mobility of said second nucleic acids; and (c) applying afirst electric field within said microfluidic chip to conductisotachophoresis in said first channel with said first trailing ions,said first nucleic acids, and said first leading ions, and applying asecond electric field to conduct isotachophoresis in said second channelwith said second trailing ions, said second nucleic acids, and saidsecond leading ions, thereby simultaneously purifying said first nucleicacids from said first contaminant and said second nucleic acids fromsaid second contaminant.

In some embodiments of aspects provided herein, said first sample andsaid second sample are different sample types. In some embodiments ofaspects provided herein, said first nucleic acids and said secondnucleic acids are different types or lengths of nucleic acids. In someembodiments of aspects provided herein, said first trailing electrolytebuffer or said first leading electrolyte buffer further comprises alysis agent or a tissue disruption agent. In some embodiments of aspectsprovided herein, said lysis agent or said tissue disruption agentcomprises one or more agents selected from the group consisting of asolution with pH greater than about 12, a proteinase, urea, thiourea,and a surfactant. In some embodiments of aspects provided herein, saidfirst sample comprises lysed solid tissue. In some embodiments ofaspects provided herein, said second sample comprises lysed cells. Insome embodiments of aspects provided herein, said first sample does notcontact said second sample during said conducting of isotachophoresis.Some embodiments of aspects provided herein further comprise loadinginto a third channel of said microfluidic chip (i) a third samplecomprising third nucleic acids and a third contaminant, (ii) a thirdtrailing electrolyte buffer comprising third trailing ions, wherein amagnitude of an effective mobility of said third trailing ions is lessthan a magnitude of an effective mobility of said third nucleic acids,and (iii) a third leading electrolyte buffer comprising third leadingions, wherein a magnitude of an effective mobility of said third leadingions is greater than said magnitude of said effective mobility of saidthird nucleic acids, wherein said electric field is applied within saidmicrofluidic chip to conduct said isotachophoresis in said third channelwith said third trailing ions, said third nucleic acids, and said thirdleading ions, thereby simultaneously purifying said first nucleic acidsfrom said first contaminant, said second nucleic acids from said secondcontaminant and said third nucleic acids from said third contaminant. Insome embodiments of aspects provided herein, said first and secondelectric fields are generated from a single electrode pair. In someembodiments of aspects provided herein, said first and second electricfields are generated from different electrode pairs. In some embodimentsof aspects provided herein, said first and second channels are coupledto independent sensors. In some embodiments of aspects provided herein,feedback from said independent sensors is used to independently controlsaid first and second electric fields. In some embodiments of aspectsprovided herein, said independent sensors sense voltage and saidfeedback is used to control current (or resistance) within said firstand second channels. In some embodiments of aspects provided herein,said nucleic acids comprise DNA. In some embodiments of aspects providedherein, said nucleic acids comprise RNA.

As aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading onto a fluidic device (i) a samplecomprising fixed cells, fixed tissue, or embedded tissue, wherein saidsample comprise nucleic acids, (ii) a trailing electrolyte buffercomprising trailing electrolytes, wherein said trailing electrolyteshave a lower effective mobility than said nucleic acids, and (iii) aleading electrolyte buffer comprising leading electrolytes, wherein saidleading electrolytes have a higher effective mobility than said nucleicacids; and (b) applying an electric field on said fluidic device toconduct isotachophoresis with said trailing electrolytes, said nucleicacids, and said leading electrolytes, thereby purifying said nucleicacids from a contaminant in said sample.

In some embodiments of aspects provided herein, said contaminant isselected from the group consisting of crosslinked nucleic acids,embedding material, fixation chemicals, enzymes, and inhibitors. In someembodiments of aspects provided herein, said sample comprises said fixedcells, said fixed tissue, or both said fixed cells and said fixedtissue. In some embodiments of aspects provided herein, said sample isformalin-fixed. In some embodiments of aspects provided herein, saidsample comprises said embedded tissue. In some embodiments of aspectsprovided herein, said sample comprises said tissue embedded in paraffin.In some embodiments of aspects provided herein, said sample is aformalin-fixed paraffin-embedded (FFPE) tissue sample. In someembodiments of aspects provided herein, said sample comprises a tissuebiopsy. In some embodiments of aspects provided herein, said sample is adissected formalin-fixed paraffin-embedded (FFPE) sample. Someembodiments of aspects provided herein further comprise comparing acharacteristic of said nucleic acids to nucleic acids from othersamples, wherein said characteristic is an expression level, a nucleicacid sequence, a molecular weight, nucleic acid integrity, nucleic-acidstranded-ness (e.g. double-versus single-stranded), or nucleic acidpurity. In some embodiments of aspects provided herein, said sample is atumor sample. In some embodiments of aspects provided herein, saidtrailing electrolyte buffer has a pH of greater than about 7. Someembodiments of aspects provided herein further comprises, prior to saidapplying said electric field, incubating said tissue sample in saidfluidic device at a temperature of at least about 37° C. for a durationof at least about 1 minute. In some embodiments of aspects providedherein, said temperature is from about 40° C. to about 80° C. In someembodiments of aspects provided herein, said duration is from about 1minute to about 120 minutes. In some embodiments of aspects providedherein, said leading electrolyte buffer comprises proteinase K. Someembodiments of aspects provided herein further comprise removing proteincrosslinks from said nucleic acids using said proteinase K. Someembodiments of aspects provided herein further comprise, after saidapplying said electric field, removing protein crosslinks from saidnucleic acids using heat. Some embodiments of aspects provided hereinfurther comprise eluting an output solution comprising said purifiednucleic acids from an outlet reservoir of said fluidic device. In someembodiments of aspects provided herein, a concentration of said purifiednucleic acids in said output solution is at least about two-fold higherthan a concentration of said nucleic acids in said tissue sample. Insome embodiments of aspects provided herein, a concentration of saidcrosslinked nucleic acids in said output solution is at least abouttwo-fold lower than a concentration of said crosslinked nucleic acids insaid tissue sample. In some embodiments of aspects provided herein, saidoutput solution has a volume equal to or less than about 50 μL. In someembodiments of aspects provided herein, said tissue sample has a mass ofat least about 1 ng. In some embodiments of aspects provided herein,said tissue sample has a volume greater than 25 μL. In some embodimentsof aspects provided herein, said trailing electrolytes have a highereffective mobility than said contaminant. In some embodiments of aspectsprovided herein, said trailing electrolytes comprise (i) first ions,wherein said first ions have a higher effective mobility magnitude thansaid contaminant, and (ii) second ions, wherein said second ions have aneffective mobility magnitude about the same as or lower than saidcontaminant. In some embodiments of aspects provided herein, saidconducting isotachophoresis quenches a pH of said tissue sample to about7.5. Some embodiments of aspects provided herein further comprise, priorto said loading, conducting de-paraffinization on said sample. Someembodiments of aspects provided herein further comprise detecting aconcentration of said nucleic acids. In some embodiments of aspectsprovided herein, said concentration is less than or equal to about 1picogram per microliter (pg/μL).

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a fluidic device (i) a tissuesample comprising lysed solid tissue and nucleic acids, (ii) a trailingelectrolyte buffer, said trailing electrolyte buffer comprising trailingelectrolyte ions with a first effective mobility, wherein said firsteffective mobility has a magnitude lower than a magnitude of aneffective mobility of said nucleic acids, (iii) a first leadingelectrolyte buffer in a first leading electrolyte reservoir, said firstleading electrolyte buffer comprising first leading electrolyte ionswith a second effective mobility, wherein said second effective mobilityhas a magnitude greater than said magnitude of said effective mobilityof said nucleic acids, and (iv) a second leading electrolyte buffer in asecond leading electrolyte reservoir, said second leading electrolytebuffer comprising second leading electrolyte ions with a third effectivemobility, wherein said third effective mobility has a magnitude greaterthan said magnitude of said effective mobility of said nucleic acids,wherein said first leading electrolyte buffer is different from saidsecond leading electrolyte buffer; (b) first conducting isotachophoresiswith said trailing electrolyte ions, said nucleic acids, and said firstleading electrolyte ions, thereby purifying said nucleic acids from saidcontaminant in said tissue sample; and (c) second conductingisotachophoresis with said trailing electrolyte ions, said nucleicacids, and said second leading electrolyte ions.

In some embodiments of aspects provided herein, said second conductingisotachophoresis comprises changing an applied current from a firstchannel to a second channel. In some embodiments of aspects providedherein, said first leading electrolyte ions are the same as said secondleading electrolyte ions, and wherein a concentration of said firstleading electrolyte ions in said first leading electrolyte buffer isdifferent from a concentration of said second leading electrolyte ionsin said second leading electrolyte buffer. In some embodiments ofaspects provided herein, said second effective mobility has a magnitudegreater than said magnitude of said third effective mobility. In someembodiments of aspects provided herein, said first leading electrolyteions are different from said second leading electrolyte ions. In someembodiments of aspects provided herein, said first leading electrolyteions are the same as said second leading electrolyte ions, and wherein aconcentration of said first leading electrolyte ions in said firstleading electrolyte buffer is the same as a concentration of said secondleading electrolyte ions in said second leading electrolyte buffer, andwherein said first leading electrolyte buffer comprises third leadingelectrolyte ions. In some embodiments of aspects provided herein, saidfirst leading electrolyte ions are the same as said second leadingelectrolyte ions, and wherein a concentration of said first leadingelectrolyte ions in said first leading electrolyte buffer is the same asa concentration of said second leading electrolyte ions in said secondleading electrolyte buffer, and wherein said second leading electrolytebuffer comprises third leading electrolyte ions. Some embodiments ofaspects provided herein further comprise collecting said nucleic acidsin said second leading electrolyte reservoir and removing said nucleicacids from said second leading electrolyte reservoir. In someembodiments of aspects provided herein, said first conductingisotachophoresis and said second conducting isotachophoresis areperformed by applying a single electric field. In some embodiments ofaspects provided herein, said first conducting isotachophoresis and saidsecond conducting isotachophoresis are performed by applying more thanone electric field. In some embodiments of aspects provided herein, theconcentration of said second leading electrolyte ions in said secondleading electrolyte buffer is less than 50 mM. In some embodiments ofaspects provided herein, said second leading electrolyte buffercomprises 50 mM Tris HCl.

An aspect of the present disclosure provides a microfluidic devicecomprising: (a) a first isotachophoresis region in a microfluidic chipcomprising: (i) a first sample reservoir in fluid communication with afirst fluidic channel, (ii) a first buffer reservoir in fluidcommunication with said first fluidic channel, and (iii) a second bufferreservoir in fluid communication with said first channel; and (b) asecond isotachophoresis region in said microfluidic chip comprising: (i)a second sample reservoir in fluid communication with a second fluidicchannel, (ii) a third buffer reservoir in fluid communication with saidsecond fluidic channel, and (iii) a fourth buffer reservoir in fluidcommunication with said second channel, wherein said firstisotachophoresis region is not in fluid communication with said secondisotachophoresis region and wherein said microfluidic device isconfigured to independently control a first electric circuit thatapplies current to said first isotachophoresis region and a secondelectric circuit that applies current to said second isotachophoresisregion.

In some embodiments of aspects provided herein, a leakage rate betweensaid first and second isotachophoresis regions is less than 1 μl perhour. In some embodiments of aspects provided herein, current leakagebetween said first and second isotachophoresis regions is less than 1μA. In some embodiments of aspects provided herein, an impedance isgreater than 1 megaOhm. In some embodiments of aspects provided herein,said first fluidic channel holds a liquid volume greater than 100 μl. Insome embodiments of aspects provided herein, said first fluidic channelis separated from said second fluidic channel by a distance that is atleast 5-fold less than a width of said first channel. In someembodiments of aspects provided herein, said microfluidic device isconfigured to control said first electric circuit simultaneously withsaid second electric circuit. Some embodiments of aspects providedherein further comprise an elution reservoir in fluid communication tosaid first channel, wherein a temperature sensor is situated within 5 mmof said elution reservoir.

An aspect of the present disclosure provides a method, comprising: (a)providing an electrokinetic fluidic device comprising a sample inputreservoir in fluid communication with a channel; (b) loading a samplevolume into said sample input reservoir; (c) moving at least 50% of saidsample volume from said sample input reservoir to said channel, withoutadding additional volume to said sample input reservoir; and (d)applying an ionic current through said channel.

In some embodiments of aspects provided herein, said moving is conductedwith aid of gravity. In some embodiments of aspects provided herein,said ionic current does not substantially pass through said channel. Insome embodiments of aspects provided herein, said at least 50% of saidsample volume comprises at least 80% of said sample volume. In someembodiments of aspects provided herein, said sample volume comprisesnucleic acids. In some embodiments of aspects provided herein, saidsample volume comprises a tissue sample or a formalin-fixedparaffin-embedded (FFPE) sample. In some embodiments of aspects providedherein, said applying an ionic current comprises conductingisotachophoresis. In some embodiments of aspects provided herein, atotal sample volume loaded into said sample input reservoir is less thanor equal to an internal volume of said input reservoir. In someembodiments of aspects provided herein, said sample input reservoircomprises a top region connected to a bottom region via a taperedregion, wherein said top region has a first diameter and said bottomregion has a second diameter, wherein said first diameter is at leasttwo-fold longer than said second diameter in order to facilitate saidmoving at least 50% of said sample volume from said sample inputreservoir to said channel. In some embodiments of aspects providedherein, said sample volume is at least 25 μl. In some embodiments ofaspects provided herein, said sample volume is at least 50 μl. In someembodiments of aspects provided herein, said sample volume is at least100 μl.

An aspect of the present disclosure provides a microfluidic chipcomprising: a first sample input reservoir, wherein said first sampleinput reservoir comprises a top region connected to a bottom region viaa tapered region, wherein said top region has a first inner hydraulicdiameter and said bottom region has a second inner hydraulic diameter,wherein said first inner hydraulic diameter is at least 2-fold longerthan said second inner hydraulic diameter and wherein said first sampleinput reservoir is in fluid communication with a first channel; a firstbuffer reservoir in fluid communication with said first channel, whereinsaid first sample reservoir is configured so that a free surface of aliquid in said first sample reservoir has a negligible buffer headheight difference relative to a liquid in said first buffer reservoir;and a second buffer reservoir in fluid communication with said firstchannel.

In some embodiments of aspects provided herein, said first innerhydraulic diameter is a range of about 1 mm to about 15 mm. In someembodiments of aspects provided herein, said second inner hydraulicdiameter is a range of about 0.5 mm to about 5 mm. In some embodimentsof aspects provided herein, said first sample reservoir is configured tohold a sample volume of at least 100 μl. In some embodiments of aspectsprovided herein, said microfluidic chip is configured to move at least50% of said sample volume from said first sample reservoir to said firstchannel when a vacuum is applied thereto. In some embodiments of aspectsprovided herein, said microfluidic chip is configured to conductisotachophoresis on a sample that enters said first channel.

An aspect of the present disclosure provides a method of extractingnucleic acids, comprising: (a) exposing a biological sample comprisingcells or tissue to a solution comprising urea or thiourea, therebylysing said cells or tissue within said biological sample and producinga cellular lysate; (b) introducing said cellular lysate into a device;and (c) performing isotachophoresis with said device in order to isolatenucleic acids from said cellular lysate.

Some embodiments of aspects provided herein further comprise digestingsaid sample with proteinase K. In some embodiments of aspects providedherein, said solution comprises urea and thiourea. In some embodimentsof aspects provided herein, said solution comprises a ratio of urea tothiourea of about 2 to 1. In some embodiments of aspects providedherein, a concentration of said urea in said solution is from about 4 Mto about 9 M and a concentration of said thiourea in said solution isfrom about 0.5 M to about 3.5 M. In some embodiments of aspects providedherein, a concentration of said urea in said solution is from about 6.5M to about 7.5 M and a concentration of said thiourea in said solutionis from about 1.5 M to about 2.5 M. In some embodiments of aspectsprovided herein, said solution comprises trailing electrolyte ions orleading electrolyte ions or both trailing electrolyte ions and leadingelectrolyte ions.

An aspect of the present disclosure provides a method of purifying highmolecular weight nucleic acids from a tissue sample, comprising: (a)loading into a fluidic device: (i) a cellular sample comprising genomicDNA and a contaminant, wherein said cellular sample is contacted with alysis buffer prior to or after said loading of said cellular sample intosaid fluidic device, (ii) a trailing electrolyte buffer, said trailingelectrolyte buffer comprising trailing electrolyte ions with a firsteffective mobility, wherein said first effective mobility has amagnitude lower than a magnitude of an effective mobility of said highmolecular weight nucleic acids and a magnitude greater than a magnitudeof said contaminant, and (iii) a first leading electrolyte buffer, saidfirst leading electrolyte buffer comprising first leading electrolyteions with a second effective mobility, wherein said second effectivemobility has a magnitude greater than said magnitude of said effectivemobility of said high molecular weight nucleic acids; (b) conductingisotachophoresis with said trailing electrolyte ions, said highmolecular weight nucleic acids, and said first leading electrolyte ions,thereby separating said high molecular weight nucleic acids from saidcontaminant and enriching said high molecular weight nucleic acids in anisotachophoresis zone; and (c) eluting said genomic DNA into a solutionin an output reservoir, wherein greater than 50% of the mass of nucleicacids within said solution are greater than 30 kilobases.

In some embodiments of aspects provided herein, said lysis buffer doesnot comprise an alkaline buffer. In some embodiments of aspects providedherein, said lysis buffer comprises octylphenol ethoxylate. In someembodiments of aspects provided herein, greater than 50% of the mass ofnucleic acids within said solution are greater than 50 kilobases.

An aspect of the present disclosure provides a method of conductingisotachophoresis, comprising: (a) providing a fluidic device comprisinga first channel in fluid communication with a sample input reservoircomprising a tissue sample comprising lysed solid tissue, a first bufferreservoir comprising a first leading electrolyte buffer, and a secondbuffer reservoir comprising a trailing electrolyte buffer; (b)contacting a first electrode to said first leading electrolyte buffer insaid first buffer reservoir; (c) contacting a second electrode to saidtrailing electrolyte buffer in said second buffer reservoir; and (d)applying an electric field within said fluidic device to conductisotachophoresis, wherein said isotachophoresis occurs without directcontact between said tissue sample and said first and second electrodes.

In some embodiments of aspects provided herein, said fluidic devicefurther comprises a third buffer reservoir in fluid communication withsaid first channel and said first buffer reservoir, said third bufferreservoir comprising a lower concentration of said first leadingelectrolyte buffer than said first buffer reservoir. In some embodimentsof aspects provided herein, said third buffer reservoir and said firstbuffer reservoir are connected by a second channel comprising one ormore capillary barriers to limit pressure-driven flow within said secondchannel and between said third buffer reservoir and said first bufferreservoir. In some embodiments of aspects provided herein, said fluidicdevice further comprises an elution reservoir. In some embodiments ofaspects provided herein, said elution reservoir is in fluidcommunication with a fourth buffer reservoir.

An aspect of the present disclosure provides a microfluidic system, saidmicrofluidic system comprising: (a) a microfluidic chip comprising afirst channel and a first reservoir in fluid communication with saidfirst channel, wherein said first channel and said first reservoir meetat a first junction; and (b) a mechanical member comprising a firsttooth, wherein said mechanical member is configured to apply mechanicalpressure to said first channel via said first tooth in order to at leastpartially close said first channel by plastic deformation of at leastone wall of said first channel and increase fluid resistance betweensaid first channel and said first reservoir.

In some embodiments of aspects provided herein, said microfluidic chipfurther comprises a second reservoir in fluid communication with saidfirst reservoir and a second channel connecting said first reservoir andsaid second reservoir, and wherein said mechanical member furthercomprises a second tooth configured to apply mechanical pressure to saidsecond channel in order to plastically close said second channel andprevent fluid communication between said first reservoir and said secondreservoir. In some embodiments of aspects provided herein, said firsttooth is configured to deliver mechanical pressure to said firstjunction in order to close said first channel by plastic deformation ofat least one wall of said first channel. In some embodiments of aspectsprovided herein, said first tooth is configured to heat said firstchannel. In some embodiments of aspects provided herein, said mechanicalmember comprises a material with a Young's modulus of elasticity greaterthan a Young's modulus of elasticity of said first channel. In someembodiments of aspects provided herein, said microfluidic system isconfigured to perform isotachophoresis. In some embodiments of aspectsprovided herein, said first tooth is thermally coupled to a heatingelement. In some embodiments of aspects provided herein, said firsttooth is heated to a temperature greater than the glass transitiontemperature of said at least one wall of said first channel. Someembodiments of aspects provided herein comprise a method of completing aprocess in a fluidic system comprising using said microfluidic system toat least partially close said first channel by plastic deformation,thereby increasing resistance to fluid flow between said first channeland said first reservoir. In some embodiments of aspects providedherein, said first tooth of said mechanical member applies a force of atleast 0.25 lbs to said first channel. In some embodiments of aspectsprovided herein, said process in said fluidic system isisotachophoresis.

An aspect of the present disclosure provides a method of performingisotachophoresis on a sample comprising nucleic acids comprising: (a)loading said sample comprising nucleic acids into a first reservoir of amicrofluidic chip; (b) loading a trailing electrolyte buffer into asecond reservoir of said microfluidic chip, wherein said trailingelectrolyte buffer comprises first trailing electrolyte ions with aneffective mobility having a magnitude lower than a magnitude of aneffective mobility of said nucleic acids; (c) loading a leadingelectrolyte buffer into a third reservoir of said microfluidic chip,wherein said third reservoir comprises first leading electrolyte ionswith a second effective mobility, wherein said second effective mobilityhas a magnitude greater than said magnitude of said effective mobilityof said nucleic acids; (d) applying an electric field within saidmicrofluidic chip to conduct isotachophoresis with said first trailingelectrolyte ions, said nucleic acids, and said first leading electrolyteions, thereby confining said nucleic acids, or a portion thereof, to anisotachophoresis zone; and (e) using a temperature sensor to sense atemperature change in or near said isotachophoresis zone, whereinfeedback from said temperature sensor is used to control said electricfield.

In some embodiments of aspects provided herein, said control of saidelectric field results in positioning of said nucleic acids, or portionthereof, in an elution reservoir or region of said microfluidic chip. Insome embodiments of aspects provided herein, said temperature sensor islocated within at most 8 mm of said elution reservoir. In someembodiments of aspects provided herein, said temperature change iswithin a range of about 0.2° C. to 5° C. In some embodiments of aspectsprovided herein, said applied electric field causes said leadingelectrolyte and said trailing electrolyte to meet at an isotachophoresisinterface and said temperature sensor senses said isotachophoresisinterface.

An aspect of the present disclosure provides a microfluidic devicecomprising: (a) a first isotachophoresis region in a microfluidic chipcomprising: (i) a first sample reservoir in fluid communication with afirst fluidic channel; (ii) a first, a second, and a third bufferreservoir in fluid communication with said first fluidic channel,wherein said first and second buffer reservoirs are separated by acapillary barrier; and (iii) an elution reservoir in fluid communicationwith said first fluidic channel; (b) a sensor configured to detect atemperature change in said first fluidic channel within said firstisotachophoresis region; and (c) an apparatus positioned to supplyelectrical current within said first channel within said firstisotachophoresis region.

Some embodiments of aspects provided herein further comprise acontroller configured to trigger a reduction or elimination of saidelectrical current when said sensor receives a thermal signal. In someembodiments of aspects provided herein, said temperature change is anincrease in temperature within a range of about 0.2° C. to 5° C. In someembodiments of aspects provided herein, said microfluidic device isfurther configured to isolate a sample of nucleic acids in said elutionreservoir after said sensor detects a change in temperature. In someembodiments of aspects provided herein, said sensing of said nucleicacids is performed with a sensor located within at most 8 mm of saidelution reservoir. In some embodiments of aspects provided herein, saidfirst channel comprises a single sensor.

An aspect of the present disclosure provides a kit comprising: (a) saidmicrofluidic device of claim 111, said microfluidic device of claim 165,or said microfluidic chip of claim 128; (b) a trailing electrolytebuffer comprising trailing electrolytes; and (c) a leading electrolytebuffer comprising leading electrolytes.

In some embodiments of aspects provided herein, said trailingelectrolyte buffer comprises a mixture of at least two electrolytes withdifferent effective mobilities. In some embodiments of aspects providedherein, said mixture comprises (i) a first electrolyte that has a lowereffective mobility magnitude than a nucleic acid and a higher effectivemobility magnitude than a contaminant, and (ii) a second electrolytewhich has a lower effective mobility magnitude than said contaminant. Insome embodiments of aspects provided herein, said first electrolytecomprises caproic acid. In some embodiments of aspects provided herein,said second electrolyte comprises HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid). In someembodiments of aspects provided herein, said kit further comprisessample buffer, wherein said sample buffer comprises leading electrolytebuffer, trailing electrolyte buffer, or urea in any combination. In someembodiments of aspects provided herein, said kit further comprises asample buffer comprising urea and thiourea.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a fluidic device (i) a tissuesample comprising nucleic acids and a contaminant, wherein said tissuesample is not an unlysed whole blood sample, (ii) a trailing electrolytebuffer comprising trailing electrolyte ions with an effective mobilityhaving a magnitude greater than a magnitude of an effective mobility ofsaid contaminant and lower than a magnitude of an effective mobility ofsaid nucleic acids, and (iii) a leading electrolyte buffer comprisingleading electrolyte ions, with a second effective mobility, wherein saidsecond effective mobility has a magnitude greater than said magnitude ofsaid effective mobility of said nucleic acids; and (b) applying anelectrical field within said fluidic device to conduct isotachophoresiswith said trailing electrolyte ions, said nucleic acids, and saidleading electrolyte ions, thereby purifying said nucleic acids from saidcontaminant in said tissue sample.

In some embodiments of aspects provided herein, said tissue sample isnot a whole blood sample. In some embodiments of aspects providedherein, said trailing electrolyte ions comprise caproic acid. In someembodiments of aspects provided herein, said leading electrolyte ionscomprise chloride. In some embodiments of aspects provided herein, saidtrailing electrolyte buffer comprises second trailing electrolyte ionshaving a different effective mobility than said first trailingelectrolyte ions. In some embodiments of aspects provided herein, saidsecond trailing electrolyte ions comprise HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid). In someembodiments of aspects provided herein, said second trailing electrolyteions comprise MOPS (3-(N-morpholino)propanesulfonic acid). In someembodiments of aspects provided herein, said second trailing electrolyteions comprise HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)and first trailing electrolyte ions are comprised of caproic acid. Insome embodiments of aspects provided herein, said second trailingelectrolyte ions comprise MOPS (3-(N-morpholino)propanesulfonic acid)and first trailing electrolyte ions are comprised of caproic acid. Insome embodiments of aspects provided herein, said second trailingelectrolyte ions comprise HEPES and first trailing electrolyte ionscomprise MOPS. In some embodiments of aspects provided herein, saidtrailing electrolyte buffer comprises second trailing electrolyte ionswith a second effective mobility, wherein said second effective mobilityhas a magnitude about the same as or lower than said magnitude of saideffective mobility of said contaminant. In some embodiments of aspectsprovided herein, said contaminant is selected from the group consistingof crosslinked nucleic acids, embedding material, fixation chemicals,proteins, inhibitors, and combinations thereof. In some embodiments ofaspects provided herein, said contaminant comprises crosslinked nucleicacids. In some embodiments of aspects provided herein, said tissuesample is combined with said trailing electrolyte buffer prior to saidloading. In some embodiments of aspects provided herein, said tissuesample is combined with said leading electrolyte buffer prior to saidloading. In some embodiments of aspects provided herein, said loading ofsaid leading electrolyte buffer is conducted prior to said loading ofsaid tissue sample. In some embodiments of aspects provided herein, themethod further comprises eluting an output solution comprising saidpurified nucleic acids from an outlet reservoir of said fluidic device.In some embodiments of aspects provided herein, a concentration of saidpurified nucleic acids in said output solution is at least abouttwo-fold higher than a concentration of said nucleic acids in saidtissue sample. In some embodiments of aspects provided herein, aconcentration of said crosslinked nucleic acids in said output solutionis at least about two-fold lower than a concentration of saidcrosslinked nucleic acids in said tissue sample. In some embodiments ofaspects provided herein, said output solution does not comprise saidcontaminant. In some embodiments of aspects provided herein, said tissuesample is fresh tissue. In some embodiments of aspects provided herein,said tissue sample is fresh frozen (FF) tissue. In some embodiments ofaspects provided herein, said tissue sample is formalin fixed paraffinembedded tissue (FFPE). In some embodiments of aspects provided herein,the method further comprises, prior to said loading, lysing ordisrupting said tissue sample. In some embodiments of aspects providedherein, said lysing or disrupting is conducted using urea or thiourea.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a first channel on a fluidicdevice (i) a first tissue sample comprising first nucleic acids and afirst contaminant, (ii) a first trailing electrolyte buffer comprisingfirst trailing ions, wherein a magnitude of an effective mobility ofsaid first trailing ions is less than a magnitude of an effectivemobility of said first nucleic acids, and (iii) a first leadingelectrolyte buffer comprising first leading ions, wherein a magnitude ofan effective mobility of said first leading ions is greater than saidmagnitude of said effective mobility of said first nucleic acids; (b)loading into a second channel on said fluidic device (iv) a secondtissue sample comprising second nucleic acids and a second contaminant,(v) a second trailing electrolyte buffer comprising second trailingions, wherein a magnitude of said second trailing ions is less than amagnitude of an effective mobility of said second nucleic acids, and(vi) a second leading electrolyte buffer comprising second leading ions,wherein a magnitude of an effective mobility of said second leading ionsis greater than said magnitude of said effective mobility of said secondnucleic acids; and (c) applying an electrical field within said fluidicdevice to conduct isotachophoresis in said first channel with said firsttrailing ions, said first nucleic acids, and said first leading ions,and to conduct isotachophoresis in said second channel with said secondtrailing ions, said second nucleic acids, and said second leading ions,thereby purifying said first nucleic acids from said first contaminantand purifying said second nucleic acids from said second contaminant.

In some embodiments of aspects provided herein, said first trailingelectrolyte buffer or said first leading electrolyte buffer furthercomprises a lysis agent or a tissue disruption agent. In someembodiments of aspects provided herein, said second trailing electrolytebuffer or said second leading electrolyte buffer further comprises alysis agent or a tissue disruption agent. In some embodiments of aspectsprovided herein, said lysis agent or said tissue disruption agentcomprises one or more agents selected from the group consisting of asolution with pH greater than about 12, a proteinase, urea, thiourea,and a surfactant.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a first zone of a fluidicdevice (i) a tissue sample comprising nucleic acids and a contaminant,(ii) a trailing electrolyte buffer comprising trailing ions, wherein amagnitude of an effective mobility of said trailing ions is lower than amagnitude of an effective mobility of said nucleic acids, and (iii) aleading electrolyte buffer comprising leading ions, wherein a magnitudeof an effective mobility of said leading ions is greater than saidmagnitude of said effective mobility of said nucleic acids; and (b)applying an electrical field on said fluidic device to conductisotachophoresis in a second zone of said fluidic device with saidtrailing ions, said nucleic acids, and said leading ions, therebypurifying said nucleic acids from said contaminant, wherein during saidapplying, said first zone is maintained at a first temperature and saidsecond zone is maintained at a second temperature different from saidfirst temperature.

In some embodiments of aspects provided herein, said trailingelectrolyte buffer or said leading electrolyte buffer further comprisesa lysis agent or a tissue disruption agent. In some embodiments ofaspects provided herein, said lysis agent or said tissue disruptionagent comprises one or more agents selected from the group consisting ofa solution with pH greater than about 12, a proteinase, urea, thiourea,and a surfactant. In some embodiments of aspects provided herein, saidfirst temperature is between about 4° C. and about 40° C. In someembodiments of aspects provided herein, said first temperature isbetween about 40° C. and about 80° C.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a first zone of a fluidicdevice (i) a tissue sample comprising nucleic acids, (ii) a trailingelectrolyte buffer comprising trailing ions, wherein a magnitude of aneffective mobility of said trailing ions is lower than a magnitude of aneffective mobility of said nucleic acids, and (iii) a leadingelectrolyte buffer comprising leading ions, wherein a magnitude of aneffective mobility of said leading ions is greater than said magnitudeof said effective mobility of said nucleic acids; (b) in said firstzone, conducting on said tissue sample at least one sample preparationselected from the group consisting of (1) removing embedding material,(2) disrupting tissue, (3) lysing cells, (4) de-crosslinking nucleicacids, (5) digesting proteins and (6) digesting nucleic acids; and (c)applying an electrical field within said fluidic device to conductisotachophoresis in a second zone of said fluidic device with saidtrailing ions, said nucleic acids, and said leading ions, therebypurifying said nucleic acids from a contaminant in said tissue sample.

In some embodiments of aspects provided herein, said removing embeddingmaterial or said lysing cells comprises, prior to said applying saidelectric field, incubating said tissue sample in said fluidic device ata temperature of at least about 37° C. for duration of at least about 1minute. In some embodiments of aspects provided herein, said temperatureis from about 40° C. to about 80° C. In some embodiments of aspectsprovided herein, said duration is from about 1 minute to about 60minutes. In some embodiments of aspects provided herein, said disruptingtissue or said lysing cells comprises applying mechanical stress to saidsample. In some embodiments of aspects provided herein, said disruptingtissue or said lysing cells comprises applying heat to said sample. Insome embodiments of aspects provided herein, said applying heat resultsin a temperature of said tissue sample from about 30° C. to about 65° C.In some embodiments of aspects provided herein, said disrupting tissueor said lysing cells comprises a solution pH of at least 12. In someembodiments of aspects provided herein, said disrupting tissue or saidlysing cells comprises proteolytic digestion. In some embodiments ofaspects provided herein, said proteolytic digestion is conducted at atemperature greater than about 25° C. In some embodiments of aspectsprovided herein, said temperature is from about 30° C. to about 65° C.In some embodiments of aspects provided herein, said disrupting tissueor said lysing cells comprises applying at least one surfactant to saidtissue or said cells. In some embodiments of aspects provided herein,said disrupting tissue or said lysing cells comprises applying asolution comprising urea to said tissue or said cells. In someembodiments of aspects provided herein, said solution further comprisesthiourea. In some embodiments of aspects provided herein, aconcentration of said urea in said solution is from about 4 M to about 9M and a concentration of said thiourea in said solution is from about0.5 M to about 3.5 M. In some embodiments of aspects provided herein, aconcentration of said urea in said solution is from about 6.5 M to about7.5 M and a concentration of said thiourea in said solution is fromabout 1.5 M to about 2.5 M. In some embodiments of aspects providedherein, said de-crosslinking nucleic acids comprises digestingcrosslinking proteins with proteinase K. In some embodiments of aspectsprovided herein, said digesting nucleic acids is performed with DNase orRNase.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading onto a fluidic device (i) a tissuesample comprising nucleic acids, wherein said tissue sample is embeddedor fixed, (ii) a trailing electrolyte buffer comprising trailingelectrolytes, wherein said trailing electrolytes have a lower effectivemobility than said nucleic acids, and (iii) a leading electrolyte buffercomprising leading electrolytes, wherein said leading electrolytes havea higher effective mobility than said nucleic acids; and (b) applying anelectrical field on said fluidic device to conduct isotachophoresis withsaid trailing electrolytes, said nucleic acids, and said leadingelectrolytes, thereby purifying said nucleic acids from a contaminant insaid tissue sample.

In some embodiments of aspects provided herein, said contaminant isselected from the group consisting of crosslinked nucleic acids,embedding material, fixation chemicals, enzymes, and inhibitors. In someembodiments of aspects provided herein, said embedding materialcomprises paraffin. In some embodiments of aspects provided herein, saidtissue sample is formalin-fixed. In some embodiments of aspects providedherein, said tissue sample is embedded and fixed. In some embodiments ofaspects provided herein, said tissue sample is a formalin-fixedparaffin-embedded (FFPE) tissue sample. In some embodiments of aspectsprovided herein, said tissue sample is a dissected tissue sample. Insome embodiments of aspects provided herein, said dissected tissuesample is dissected FFPE sample. In some embodiments of aspects providedherein, the method further comprises the step of comparing acharacteristic of said nucleic acids to nucleic acids from othersamples. In some embodiments of aspects provided herein, saidcharacteristic is an expression level. In some embodiments of aspectsprovided herein, said characteristic is a nucleic acid sequence. In someembodiments of aspects provided herein, said characteristic is amolecular weight. In some embodiments of aspects provided herein, saidcharacteristic is a nucleic acid integrity. In some embodiments ofaspects provided herein, said characteristic is a nucleic acid purity.In some embodiments of aspects provided herein, the method furthercomprises a step of administering a drug based on said characteristic ofsaid nucleic acids. In some embodiments of aspects provided herein, saidtissue sample is a tumor sample. In some embodiments of aspects providedherein, said trailing electrolyte buffer has a pH of about 7. In someembodiments of aspects provided herein, said trailing electrolyte bufferhas a pH of greater than about 7. In some embodiments of aspectsprovided herein, the method further comprises, prior to said applyingsaid electric field, incubating said tissue sample in said fluidicdevice at a temperature of at least about 37° C. for duration of atleast about 1 minute. In some embodiments of aspects provided herein,said temperature is from about 40° C. to about 80° C. In someembodiments of aspects provided herein, said duration is from about 1minute to about 60 minutes. In some embodiments of aspects providedherein, said leading electrolyte buffer comprises proteinase K. In someembodiments of aspects provided herein, the method further comprisesremoving protein crosslinks from said nucleic acids using saidproteinase K. In some embodiments of aspects provided herein, the methodfurther comprises, after said applying said electric field, removingprotein crosslinks from said nucleic acids using heat. In someembodiments of aspects provided herein, the method further compriseseluting an output solution comprising said purified nucleic acids froman outlet reservoir of said fluidic device. In some embodiments ofaspects provided herein, a concentration of said purified nucleic acidsin said output solution is at least about two-fold higher than aconcentration of said nucleic acids in said tissue sample. In someembodiments of aspects provided herein, a concentration of saidcrosslinked nucleic acids in said output solution is at least abouttwo-fold lower than a concentration of said crosslinked nucleic acids insaid tissue sample. In some embodiments of aspects provided herein, saidoutput solution does not comprise said contaminant. In some embodimentsof aspects provided herein, said output solution has a volume equal toor less than about 50 μL. In some embodiments of aspects providedherein, said tissue sample has a mass of at least about 1 ng. In someembodiments of aspects provided herein, said tissue sample has a volumeof less than about 500 μL. In some embodiments of aspects providedherein, said trailing electrolytes have a higher effective mobility thansaid contaminant. In some embodiments of aspects provided herein, saidtrailing electrolytes comprise (i) first ions, wherein said first ionshave a higher effective mobility magnitude than said contaminant, and(ii) second ions, wherein said second ions have an effective mobilitymagnitude about the same as or lower than said contaminant. In someembodiments of aspects provided herein, said conducting isotachophoresisquenches a pH of said tissue sample to about 7. In some embodiments ofaspects provided herein, the method further comprises, prior to saidloading, conducting de-paraffinization on said tissue sample. In someembodiments of aspects provided herein, said tissue sample is ahistorical formalin-fixed paraffin-embedded (FFPE) sample, furthercomprising comparing a characteristic of said nucleic acids to acharacteristic of different nucleic acids from a different tissuesample. In some embodiments of aspects provided herein, the methodfurther comprises a step of detecting a concentration of said nucleicacids. In some embodiments of aspects provided herein, saidconcentration is less than or equal to about 1 picogram per microliter(pg/μL). In some embodiments of aspects provided herein, saidconcentration is less than or equal to about 0.5 pg/μL. In someembodiments of aspects provided herein, said concentration is at leastabout 1 picogram per microliter (pg/μL).

An aspect of the present disclosure provides a fluidic device,comprising: a sample purification region, comprising: (a) a first zone;(b) a sample inlet located in said first zone; (c) a trailingelectrolyte reservoir in fluid communication with said first zone; (d) asecond zone in fluid communication with said first zone; (e) a leadingelectrolyte reservoir in fluid communication with said second zone; (f)a sample outlet in fluid communication with said second zone; (g) afirst heater in thermal communication with said first zone; and (h) asecond heater configured to transfer heat to said second zone, whereinsaid first zone is substantially thermally isolated from said secondzone.

An aspect of the present disclosure provides a fluidic device,comprising: a sample purification region, comprising: (a) a first zone;(b) a sample inlet located in said first zone; (c) a trailingelectrolyte reservoir in fluid communication with said first zone; (d) asecond zone in fluid communication with said first zone; (e) a leadingelectrolyte reservoir in fluid communication with said second zone; (f)a sample outlet in fluid communication with said second zone; and (g) aheater in thermal communication with said first zone and said secondzone.

In some embodiments of aspects provided herein, the device furthercomprises a second sample purification region. In some embodiments ofaspects provided herein, said first zone is a de-paraffinization zone.In some embodiments of aspects provided herein, said first zone is adisruption zone. In some embodiments of aspects provided herein, saidsecond zone is an isotachophoresis zone. In some embodiments of aspectsprovided herein, said first zone or said second zone has a width of lessthan about 1 mm. In some embodiments of aspects provided herein, saidfirst zone or said second zone has a width of less than about 0.5 mm.

An aspect of the present disclosure provides a kit, comprising a deviceprovided herein, a trailing electrolyte buffer comprising trailingelectrolytes, and a leading electrolyte buffer comprising leadingelectrolytes.

In some embodiments of aspects provided herein, said trailingelectrolyte buffer contains a mixture of at least two electrolytes withdifferent effective mobilities. In some embodiments of aspects providedherein, said mixture comprises (i) a first electrolyte that has a lowereffective mobility magnitude than a nucleic acid and a higher effectivemobility magnitude than a contaminant, and (ii) a second electrolytewhich has a lower effective mobility magnitude than said contaminant. Insome embodiments of aspects provided herein, said contaminant comprisescrosslinked nucleic acids. In some embodiments of aspects providedherein, said first electrolyte comprises caproic acid. In someembodiments of aspects provided herein, said second electrolytecomprises HEPES.

An aspect of the present disclosure provides a method for samplepurification, comprising: (a) loading into a fluidic device (i) a tissuesample comprising nucleic acids, (ii) a trailing electrolyte buffer,said trailing electrolyte buffer comprising trailing electrolyte ionswith a first effective mobility, wherein said first effective mobilityhas a magnitude lower than a magnitude of an effective mobility of saidnucleic acids, (iii) a first leading electrolyte buffer in a firstleading electrolyte reservoir, said first leading electrolyte buffercomprising first leading electrolyte ions with a second effectivemobility, wherein said second effective mobility has a magnitude greaterthan said magnitude of said effective mobility of said nucleic acids,and (iv) a second leading electrolyte buffer in a second leadingelectrolyte reservoir, said second leading electrolyte buffer comprisingsecond leading electrolyte ions with a third effective mobility, whereinsaid third effective mobility has a magnitude greater than saidmagnitude of said effective mobility of said nucleic acids, wherein saidfirst leading electrolyte buffer is different from said second leadingelectrolyte buffer; (b) first conducting isotachophoresis with saidtrailing electrolyte ions, said nucleic acids, and said first leadingelectrolyte ions, thereby purifying said nucleic acids from saidcontaminant in said tissue sample; and (c) second conductingisotachophoresis with said trailing electrolyte ions, said nucleicacids, and said second leading electrolyte ions.

In some embodiments of aspects provided herein, said second conductingisotachophoresis comprises changing an applied current from a firstchannel to a second channel. In some embodiments of aspects providedherein, said first leading electrolyte ions are the same as said secondleading electrolyte ions, and wherein a concentration of said firstleading electrolyte ions in said first leading electrolyte buffer isdifferent from a concentration of said second leading electrolyte ionsin said second leading electrolyte buffer. In some embodiments ofaspects provided herein, said concentration of said first leadingelectrolyte ions in said first leading electrolyte buffer is differentfrom said concentration of said second leading electrolyte ions in saidsecond leading electrolyte buffer by a factor of at least 1.5×. In someembodiments of aspects provided herein, said first leading electrolyteions are different from said second leading electrolyte ions. In someembodiments of aspects provided herein, said first leading electrolyteions are the same as said second leading electrolyte ions, and wherein aconcentration of said first leading electrolyte ions in said firstleading electrolyte buffer is the same as a concentration of said secondleading electrolyte ions in said second leading electrolyte buffer, andwherein said first leading electrolyte buffer comprises third leadingelectrolyte ions. In some embodiments of aspects provided herein, saidfirst leading electrolyte ions are the same as said second leadingelectrolyte ions, and wherein a concentration of said first leadingelectrolyte ions in said first leading electrolyte buffer is the same asa concentration of said second leading electrolyte ions in said secondleading electrolyte buffer, and wherein said second leading electrolytebuffer comprises third leading electrolyte ions. In some embodiments ofaspects provided herein, the method further comprises collecting saidnucleic acids in said second leading electrolyte reservoir. In someembodiments of aspects provided herein, the method further comprisesremoving said nucleic acids from said second leading electrolytereservoir. In some embodiments of aspects provided herein, said trailingelectrolyte buffer is loaded into a trailing electrolyte reservoir thatis separate from said first leading electrolyte reservoir and saidsecond leading electrolyte reservoir. In some embodiments of aspectsprovided herein, said first conducting isotachophoresis and said secondconducting isotachophoresis are performed by applying one electricfield. In some embodiments of aspects provided herein, said firstconducting isotachophoresis and said second conducting isotachophoresisare performed by applying more than one electric field.

An aspect of the present disclosure provides a fluidic device,comprising: a sample purification region, comprising: (a) a channelcomprising a first zone and a second zone in fluid communication withsaid first zone; (b) a sample inlet, a trailing electrolyte reservoircomprising a trailing electrolyte buffer, and a first leadingelectrolyte reservoir comprising a first leading electrolyte buffer,each in fluid communication with said first zone; and (c) a secondleading electrolyte reservoir comprising a second leading electrolytebuffer, wherein said second leading electrolyte buffer is in fluidcommunication with said second zone and wherein said second leadingelectrolyte buffer is different from said first leading electrolytebuffer.

In some embodiments of aspects provided herein, said sample inlet iscapable of receiving a sample comprising at least some non-liquidbiological material. In some embodiments of aspects provided herein,said second leading electrolyte buffer comprises a different leadingelectrolyte co-ion than said first leading electrolyte buffer. In someembodiments of aspects provided herein, said first leading electrolytebuffer comprises first leading electrolyte ions and said second leadingelectrolyte buffer comprises second leading electrolyte ions that arethe same as said first leading electrolyte ions, and wherein aconcentration of said first leading electrolyte ions in said firstleading electrolyte buffer is different from a concentration of saidsecond leading electrolyte ions in said second leading electrolytebuffer. In some embodiments of aspects provided herein, said firstleading electrolyte buffer comprises first leading electrolyte ions andsaid second leading electrolyte buffer comprises second leadingelectrolyte ions, and wherein said concentration of said first leadingelectrolyte ions in said first leading electrolyte buffer is differentfrom said concentration of said second leading electrolyte ions in saidsecond leading electrolyte buffer by a factor of at least 1.5×. In someembodiments of aspects provided herein, said first leading electrolytebuffer comprises first leading electrolyte ions and said second leadingelectrolyte buffer comprises second leading electrolyte ions that aredifferent from said first leading electrolyte ions. In some embodimentsof aspects provided herein, said first leading electrolyte buffercomprises first leading electrolyte ions and said second leadingelectrolyte buffer comprises second leading electrolyte ions that arethat same as said first leading electrolyte ions, and wherein aconcentration of said first leading electrolyte ions in said firstleading electrolyte buffer is the same as a concentration of said secondleading electrolyte ions in said second leading electrolyte buffer, andwherein said first leading electrolyte buffer comprises third leadingelectrolyte ions. In some embodiments of aspects provided herein, saidfirst leading electrolyte buffer comprises first leading electrolyteions and said second leading electrolyte buffer comprises second leadingelectrolyte ions that are the same as said first leading electrolyteions, and wherein a concentration of said first leading electrolyte ionsin said first leading electrolyte buffer is the same as a concentrationof said second leading electrolyte ions in said second leadingelectrolyte buffer, and wherein said second leading electrolyte buffercomprises third leading electrolyte ions.

An aspect of the present disclosure provides a method, comprising: (a)providing an electrokinetic fluidic device comprising a reservoir influidic communication with a channel; (b) loading a sample volume intosaid reservoir; (c) moving at least 50% of said sample volume from saidreservoir to said channel; and (d) applying an ionic current throughsaid channel.

In some embodiments of aspects provided herein, said moving is conductedwith the aid of gravity. In some embodiments of aspects provided herein,said ionic current does not substantially pass through said reservoir.In some embodiments of aspects provided herein, said at least 50% ofsaid sample volume comprises at least 80% of said sample volume. In someembodiments of aspects provided herein, said sample volume comprisesnucleic acids. In some embodiments of aspects provided herein, saidsample volume comprises a tissue sample. In some embodiments of aspectsprovided herein, said sample volume comprises a formalin-fixedparaffin-embedded (FFPE) sample. In some embodiments of aspects providedherein, said applying an ionic current comprises conductingisotachophoresis (ITP).

Additional aspects and advantages of the present disclosure will becomereadily apparent to those skilled in this art from the followingdetailed description, wherein only illustrative embodiments of thepresent disclosure are shown and described. As will be realized, thepresent disclosure is capable of other and different embodiments, andits several details are capable of modifications in various obviousrespects, all without departing from the disclosure. Accordingly, thedrawings and description are to be regarded as illustrative in nature,and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference in their entiretiesto the same extent as if each individual publication, patent, or patentapplication was specifically and individually indicated to beincorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1A shows an exemplary protocol for sample processing and nucleicacid extraction or purification.

FIG. 1B shows an exemplary protocol for automated sample processing andnucleic acid extraction or purification.

FIG. 2A shows an exemplary schematic of isotachophoretic separation andpurification of DNA and RNA from contaminants.

FIG. 2B shows an exemplary schematic of isotachophoretic separation andpurification of nucleic acids from paraffin and other possible samplecontaminants concurrent with proteinase-mediated tissue disruption anddecrosslinking of nucleic acids.

FIG. 3 shows exemplary results of DNA extraction and purification byautomated isotachophoresis in a fluidic device compared to exemplaryresults from a typical solid phase column extraction kit.

FIG. 4A shows exemplary results for unbiased (e.g., with respect tosequence) extractions of GC-rich and AT-rich synthetic DNAoligonucleotides mixed at sample concentration ratios usingisotachophoresis.

FIG. 4B shows exemplary results for unbiased (e.g., with respect to sizeor molecular weight), pre- and post-purification, of a DNA molecularweight ladder using isotachophoresis; comparisons to two solid phasecolumn based nucleic acid purification methods are shown.

FIG. 5A shows an exemplary schematic of a channel with a samplepreparation zone and an isotachophoretic purification zone.

FIG. 5B shows an exemplary fluidic device cartridge comprising eightparallel fluidic channels and reservoirs for simultaneous processing ofup to eight samples as shown in FIG. 5A.

FIG. 5C shows an exemplary top view schematic of one channel and itsconnected reservoirs for a fluidic device cartridge as shown in FIG. 5B,further exemplifying use of gas ports for external pressure or vacuumapplication to the channels within the fluidic device cartridge.

FIG. 5D shows an exemplary side view schematic of a fluidic devicecartridge as shown in FIG. 5B.

FIG. 5E shows an exemplary end view schematic of a fluidic devicecartridge as shown in FIG. 5B.

FIG. 6A shows an exemplary top view schematic of a fluidic devicecartridge.

FIG. 6B shows an exemplary side view schematic of a fluidic devicecartridge.

FIG. 6C shows an exemplary bottom view schematic of a fluidic devicecartridge.

FIG. 6D shows an exemplary top full view schematic in three dimensionsof a fluidic device cartridge.

FIG. 7A shows an exemplary top view schematic of a fluidic devicecartridge.

FIG. 7B shows an exemplary side view schematic of a fluidic devicecartridge.

FIG. 7C shows an exemplary bottom view schematic of a fluidic devicecartridge.

FIG. 7D shows an exemplary bottom full view schematic in threedimensions of a fluidic device cartridge.

FIG. 8A shows an exemplary top view schematic of a fluidic devicecartridge.

FIG. 8B shows an exemplary side view schematic of a fluidic devicecartridge.

FIG. 8C shows an exemplary bottom view schematic of a fluidic devicecartridge.

FIG. 8D shows an exemplary bottom full view schematic in threedimensions of a fluidic device cartridge.

FIG. 9A shows an exemplary schematic of fluidic device cartridgecomprising eight parallel channels as shown in FIG. 5B.

FIG. 9B shows an exemplary schematic of two thermal controllers, eachaligned with a zone of the eight parallel channels shown in FIG. 9A.

FIG. 10A shows an exemplary gas channel which may comprise a capillarybarrier.

FIG. 10B is a magnified schematic of the gas channel of FIG. 10A.

FIG. 11 shows an exemplary low-loss sample reservoir.

FIG. 12A shows an exemplary mechanical member which can be used to applypressure to close the channels of a fluidic device.

FIG. 12B shows an exemplary comb-like mechanical member.

FIG. 12C shows the alignment of a comb-like mechanical member and thechannels of a fluidic device.

FIG. 13A shows an exemplary benchtop device for conducting automatedsample preparation and isotachophoresis on a fluidic device cartridge.

FIG. 13B shows an exemplary computer control system that is programmedor otherwise configured to implement methods provided herein.

FIG. 14 shows exemplary results of fluorescence-based measurements andquantitation for a titration series of nucleic acids usingisotachophoresis.

FIG. 15 shows a schematic of an exemplary design of a fluidic channelwith connected reservoirs, contactless electrode(s) (may be used asconductivity sensor) and gas port(s) for conducting automated fluidloading into channel/device and automated isotachophoresis.

FIG. 16 shows a graph of voltage measurement over time in an ITP channelduring a run.

FIG. 17 shows two graphs of derivative analysis of the voltagemeasurements from FIG. 16.

FIG. 18 shows an example of conductivity measurement over time in an ITPchannel near an elution reservoir.

FIG. 19 shows an exemplary schematic of a C4D sensor implementation.

FIG. 20A shows an exemplary temperature map of an ITP channel takenusing a thermal imaging camera.

FIG. 20B shows a plot of temperature over time at the position of Cursor1 in FIG. 20A.

FIG. 21 shows a graph of temperature measurement and temperaturederivative over time during an ITP run.

FIG. 22A shows an exemplary schematic of a vertical (or column) ITPsetup.

FIG. 22B shows an exemplary image of a vertical ITP set up with an DNAITP band.

FIG. 23 shows exemplary images and corresponding fluorescence intensitytraces of extraction and separation of amplifiable (e.g., decrosslinked)DNA from crosslinked DNA from an FFPE sample using isotachophoresis.

FIG. 24A shows an exemplary image of DNA extraction and purificationfrom FFPE samples using isotachophoresis.

FIG. 24B shows exemplary DNA yields measured by quantitative PCR forextraction and purification of DNA from FFPE samples usingisotachophoresis compared to exemplary results from a typical solidphase column extraction kit.

FIG. 25A shows an image of a single channel ITP chip loaded with nucleicacid (RNA extraction and digest from human cells) stained with dye forvisualization.

FIG. 25B shows an image of a single channel ITP chip loaded with nucleicacid (RNA extraction and digest from human cells) stained with dye forvisualization.

FIG. 26A shows an image of an RNA ITP band in a chip channel duringpurification.

FIG. 26B shows an image of a total nucleic acid ITP band in a chipchannel during purification.

FIG. 26C shows a graph of an RNA quality electropherogram for the sampleshown in FIG. 26A.

FIG. 26D shows a graph of an RNA quality electropherogram for the sampleshown in FIG. 26B.

FIG. 27A shows results of DNA yield (ng) for ITP (square) compared tocolumn (diamond, Qiagen QiaAmp) extraction of whole mouse blood as afunction of percent by volume of whole blood in starting sample.

FIG. 27B shows an image of total nucleic acid in an ITP band during ITPpurification of lysed whole mouse blood on a chip.

FIG. 27C and FIG. 27D show white light and fluorescence overlay imagesof ITP chip channels showing physical separation of heme in thesample/leading electrolyte channel from the elution channel andreservoir, before and after ITP purification of 50% by volume wholeblood lysate. Nucleic acid is stained with green dye for visualizationin elution well. FIG. 27C shows the chip before ITP (blood lysate andITP buffers loaded in chip; buffer only in elution well).

FIG. 27D shows the chip after ITP (blood lysate and ITP buffers loadedin chip; purified DNA in elution well).

FIG. 27E shows an chip post ITP purification (50% by volume blood).

FIG. 27F shows an chip post ITP purification (25% by volume blood).

FIG. 28 shows results of high molecular weight DNA purification for ITPcompared to solid phase extraction.

FIG. 29A shows a fluidic device comprising 8 closed channels.

FIG. 29B shows a zoomed in microscopic view the second channel closurelocation adjacent the elution reservoir of each of the channels.

FIG. 29C shows the percent closure calculated as a function of forceapplied to the fluidic device.

FIG. 29D shows the results of conductivity measurements of channelclosure.

FIG. 30 a graph of voltage measurement and voltage derivative over timeduring an ITP run.

FIG. 31A shows a micrograph of ITP bands with focused DNA in each of 8samples in the sample channel region of the device.

FIG. 31B shows independent voltage signal data at fixed currents foreach of the 8 channels over time.

FIG. 31C shows a micrograph of the same 8 ITP bands with focused DNAfrom the samples eluted in the elution reservoir.

FIG. 31D is a magnified section of the voltage tracing (monitoring) usedfor triggering shown in FIG. 31B.

DETAILED DESCRIPTION

Overview

Sample preparation is a first step to almost all genomic andtranscriptomic analyses, and yet can be a primary source of analysisvariability. Sample preparation can also be manually intensive,particularly when the sample is a formalin-fixed paraffin-embedded(FFPE) sample containing cross-linked proteins.

The present disclosure provides processes and devices to improve theefficiency of nucleic acid extraction and purification from tissue andcellular samples, including samples that have been processed in someway, such as paraffin-embedded samples or chemically-fixed samples(e.g., FFPE samples, samples that contain solid tissue). Methodsprovided herein include methods of on-chip or off-chip preparation ofsuch processed samples prior to conducting isotachophoresis usingmethods that incorporate leading electrolyte ions and trailingelectrolyte ions. In some instances, the methods include treating (e.g.,by removal of embedding material, lysis, enzymatic disruption) a fixedsolid tissue in a trailing electrolyte buffer or leading electrolytebuffer prior to conducting isotachophoresis on the sample. The methodscan also include use of a second leading electrolyte buffer of lowerionic strength in order to produce a sample compatible with downstreamprocesses like amplification or other enzymatic assays. The devices andsystems provided herein include devices suitable for conductingisotachophoresis on samples derived from tissues, including microfluidicdevices with parallel processing features and automated feedback-controlmechanisms that may include thermal sensors that detect changes intemperature within sample processing channels.

The processes and devices of the present disclosure can provide improvednucleic acid recovery from a sample, especially from low abundancesamples (e.g., less than 100 ng of nucleic acid), samples withrelatively high volumes (e.g., total volume greater than 25 total volumegreater than 50 total volume greater than 100 or more) or liquid samplescontaining solid particles. The processes and devices provided hereinalso can provide high repeatability, and reduced bias for short nucleicacids. The devices provided herein can integrate sample preparation(e.g., removal of crosslinking or embedding material) and nucleic acidextraction operations within one device. Devices and processes of thepresent disclosure can also provide for compatibility with processautomation, integration with downstream processes, integration within-line quantitation (e.g., at single picogram resolution), and/orintegration with nucleic acid length and sequence distribution analysis.

The methods provided herein are often methods of performingisotachophoresis under conditions suitable to extract nucleic acids fromcertain samples, especially FFPE samples. In some instances, thedisclosed methods include methods of performing isotachophoresis using atrailing electrolyte buffer containing at least two ions with differentmagnitudes of effective mobilities. The methods may also include methodsof conducting isotachophoresis using two different leading electrolytebuffers, one of which may serve as a sample elution buffer. The methodscan include process automation and parallel processing of multiplesamples.

The present disclosure also includes protocols using buffer and spacerchemistries. These buffer and spacer chemistries can include the use ofmultiple species of electrolytes for conducting ITP. For example, thetrailing electrolytes can comprise a mixture of electrolyte species,capable of separating non-crosslinked nucleic acids from crosslinkednucleic acids, while separating either non-crosslinked nucleic acids orboth crosslinked and non-crosslinked nucleic acids from contaminantswithin a sample.

The devices provided herein include injection-molded fluidic deviceswith parallel sample processing channels capable of performing ITP in amultiplexed fashion and ITP devices with two or more regions that areconnected to a thermal device. Techniques of the present disclosure canemploy ITP to simultaneously collect, purify, and focus extracted RNAand DNA, to quantify total extracted nucleic acid on-chip (e.g., viain-line ITP-aided concentration into very small volumes or labeling withan intercalating fluorescent dye), and to deliver nucleic acidsdownstream to parallel output reservoirs compatible with roboticpipetting.

Techniques of the present disclosure can enable purification of samplematerial (e.g., nucleic acids) without binding the sample material to asolid support. Techniques of the present disclosure can enablepurification of sample material (e.g., nucleic acids) without the use ofliquid-phase extraction. This can enable purification without dependenceon solubility differences.

The operation of devices of the present disclosure can be automated,largely automated, or partly automated. In some cases, methods of thepresent disclosure involve only a single off-chip mixing step ofdispensing a sample (e.g., FFPE section) into a solution (e.g., alkalinesolution, lysis solution, or buffered solution comprising urea and/orthourea), followed by loading of the sample into a reservoir of afluidic device for further on-device sample preparation (e.g.deparaffinization, tissue disruption and cell lysing, proteasedigestion, proteolytic digestion, or other treatment including proteindenaturation, or nuclease digestion) and nucleic acid extraction,purification, enrichment, in-line quantitation, and sizing orfractionation (e.g., size selection). In some cases, methods of thepresent disclosure include dispensing a sample (e.g., FFPE section orother tissue sample) into a reservoir or channel of a fluidic device(e.g., cartridge) pre-filled with a solution (e.g., alkaline solution,lysis solution, or buffered solution comprising urea and/or thourea) foron-device sample preparation (e.g. deparaffinization, tissue disruptionand cell lysing, protease digestion or other treatment including proteindenaturation, or nuclease digestion) and nucleic acid extraction,purification, enrichment, in-line quantitation, and sizing orfractionation (e.g., size selection). In some cases, methods of thepresent disclosure include disruption tissue and/or lysing cells of asample off-chip, followed by loading of the sample, which may behomogenous or a non-homogenous mixture of lysed solid tissue and nucleicacids, into a reservoir of a fluidic device for further on device samplepreparation (e.g. deparaffinization, protease digestion or othertreatment including protein denaturation, or nuclease digestion) andnucleic acid extraction, purification, enrichment, in-line quantitation,and sizing or fractionation (e.g., size selection). Nuclease digestioncan include removal of DNA for DNA-free RNA extractions or removal ofRNA for RNA-free DNA extractions. The fluidic devices provided hereincan be used with a benchtop system to automate an electric-field-basedmethod for the extraction of DNA and RNA from samples.

Devices of the present disclosure include systems that can automate andintegrate on-chip heating (e.g., to a temperature from 37° C. to 80°C.), sample preparation (e.g., deparaffinization, tissue disruption andcell lysing), buffer exchange, nucleic acid extraction and purification,enrichment of uncrosslinked or amplifiable nucleic acids (e.g., byseparating it away and delivering it separately from crosslinked nucleicacids), and delivery of purified nucleic acids to an output reservoir,such as an array compatible with manual or robotic pipetting. Forexample, the present disclosure includes an eight-channel cartridge in astandard, robotic automation compatible microtiter plate format, as wellas integrated benchtop controller prototypes that can afford automatedcontrol of loading of buffers and other fluids, application oftemperature and electric fields to the device, and automated start andend run processing of samples in parallel. This system can be easilymodified in the future, as needed, to afford higher throughput for usein larger, diagnostic or clinical labs (e.g., 96-well sample format).

For example, FIG. 1A shows an exemplary process diagram for sampleprocessing and nucleic acid extraction using techniques of the presentdisclosure. A sample can be provided 101 and subjected to anypre-processing steps 102, such as mixing with a buffer, lysis, orremoval of embedding material (if present). The sample (and, forexample, buffer) can then be loaded onto a fluidic device 103. Samplepreparation steps 104 can then be performed on the fluidic device, suchas removal of embedding material (if present and if not previouslyremoved during pre-processing), tissue disruption, cell lysis, proteinor proteolytic digestion and (for example) nuclease digestion.Isotachophoresis 105 can then be performed to separate and purifynucleic acids from contaminants within the sample (e.g. cell debris,embedding material, crosslinked nucleic acids, fixatives such asformalin, inhibitors, enzymes such as digestion or restriction enzymes).Other steps can occur concurrently with isotachophoresis, such asde-crosslinking of crosslinked nucleic acids (e.g. with heat or proteasedigestion). Nucleic acids can be detected and quantified 106 during orsubsequent to isotachophoresis. Once extracted or purified, nucleicacids can then be eluted and recovered from the device 107.

FIG. 1B shows an exemplary process workflow for automated ITP. At step110, a protocol can be selected, such as by using a graphical userinterface on a benchtop device. The user interface software can enableease of use or hands-free operation. For example, a user can select froma menu (e.g., drop-down menu). Alternatively, the device can scan abarcode (e.g., optical barcode, RFID chip) associated with a sample or afluidic device chip which can indicate the protocol to be performed. Atstep 111, the instrument lid can be opened (e.g., manually orautomatically via motor). Motorized lid opening can be compatible withrobotic laboratory automation. At step 112, the user can load a chip(e.g., fluidic device) onto the benchtop instrument. The chip cancomprise a monolithic, multichannel SLAS standard microtiter plate (MTP)footprint for automated ITP. At step 113, ITP liquids can be loaded intothe chip wells. Reservoirs for ITP fluids and user samples can bedesigned for ease of loading, such as via a multichannel pipet (e.g., 9mm pitch SLAS standard microtiter plate format). Geometrical designs(e.g., capillary barriers) of the channels connecting reservoirs to theITP channel can resist gravimetric flow or wetting of liquids into thechannel prior to operation. These structures can stop fluids in definedplaces within the ITP channel, including establishing the leadingelectrolyte/trailing electrolyte interface, as well as enablebubble-free loading. In some cases, prior to operation, pneumaticactuation can be applied to prime the channel. Chip material can beselected to prevent or resist wetting or wicking of fluids into channels(e.g., plastic with hydrophobic properties or a high contact angle). Theuser can load ITP reagents and buffers onto the chip (e.g., 5 differentfluids); alternatively, the chip can be provided with reagentspreloaded. At step 114, the user or the device can close the device lid.Sample loading can be actuated through gas or air ports on the chip.Wetting and/or gravity flow can be used to fill channels with liquids,for example without active pressure application.

At step 115, the instrument can apply pressure to load fluids in thechip to prime the channels. At step 116, the device can check that thechannels have been appropriately primed. For example, optical (e.g.,reflectance), electrical, pressure, and/or flow rate sensors can be usedto check that fluids have been loaded to the correct locations withinthe chip. Sensors and device software can enable real time monitoringand control of liquid loading. ITP reagent and buffer loading can beconducted prior to loading sample onto the chip, so that in case ofmis-loading, sample material is not wasted. If the channels are notappropriately primed, the device can perform error reporting 130. Atstep 117, the device lid can be opened. At step 118, the sample can beloaded onto the device. Sample loading can be performed manually by auser, or can be performed in an automated manner, such as via laboratoryautomation robotics. Other sample preparation steps can also beconducted. For example, a paraffin-embedded sample (e.g., FFPE) can beloaded, and then the device can control the temperature within thesample reservoir to deparaffinize the sample. At step 119, the devicelid can be closed. At step 120, the device can perform a self-test. Forexample, electrical feedback from device electrodes interfacing withon-chip reservoirs can be used to self-test for successful priming ofliquids (e.g., bubble detection). Optical sensors can be used to enablefeedback on liquid priming status (e.g., whether or not a liquid hasreached a designated capillary barrier). Other sensing mechanisms, suchas those disclosed herein, can also be used. If the self-test determinesthat the device is not properly primed, the device can perform errorreporting 131.

At step 121, ITP-based purification can be conducted. Feedback controland process timing using sensors (e.g. triggering) as described hereincan be used to control and/or automate the ITP purification. The devicecan determine whether purification was successfully performed, and ifnot, the device can perform error reporting 132. At step 122, sensors onthe device (e.g., optical sensors) can be used to quantitate thesamples, for example by fluorescence, UV, or other optical detection.Sample sizing can also be performed. If the device determines that thesample was not properly quantitated or discovers other issues, thedevice can perform error reporting 133. At step 123, a conductivitychange can be detected, which can be used to indicate timing for endingthe ITP run (e.g., when the nucleic acids reach a designated elutionlocation or reservoir). Other detection methods described herein, suchas temperature or driving voltage, can also be used to determine end ofrun timing or other triggers. For example, a temperature or voltagesensor may be used to control an electric field applied to a channelwithin the device in order to automate the ITP process. As an example,an electric field may be applied to a channel to begin ITP purification.A sensed change in voltage may be used to trigger the start oftemperature or other sensing at a fixed location within the channel suchas at or near the elution reservoir. The voltage may change as the ITPzone comprising confined nucleic acids moves. Changes indicative of theITP zone passing through channel features such as a section of decreasedcross-sectional area may be sensed by a voltage sensor and feedback maybe used to alter the electric field, for example by reducing the appliedcurrent. A change in temperature may be detected as the ITP zone passesa temperature sensor at or near the elution reservoir and feedback fromthe sensor may be used to control the electric field, for example byremoving it to end the ITP run. At step 124, the device can terminatethe run, for example based on a trigger signal. The nucleic acids may bepositioned or isolated within the elution reservoir or region when theITP run is terminated. At step 125, the device can close the channels,which can fix the elution volume to maintain a constant volume for theelution (e.g., by resisting or preventing flow into the elutionreservoir or outlet reservoir during pipetting out of the elutedvolume). Fixing the elution volume can aid ease of use and can help forreporting the concentration of the eluted sample material. At step 126,the device lid can be opened (e.g., by a user or automatically).

At step 127, purified samples can be extracted from the device. Chipsand/or devices can be designed for a given elution volume, as discussedherein. Retrieval of purified material from the device can be performedvia pipetting or otherwise removing the material from the chip.Alternatively, sample extraction can be performed by interfacing the ITPchip with another fluidic chip or system (e.g., in the absence of anelution reservoir). Other fluidic systems can then be used to performother operations on the purified sample material, such as nextgeneration sequencing (NGS) library preparation, sample analysis such asPCR, ddPCR, other sequencing operations, or other downstream processes.At step 128, the device can report quantitative data about the sample,such as sample amount and/or sample concentration. The device cancontain an algorithm or other software for converting a measurement(e.g., a fluorescence signal) into a sample quantitation, and can reportthat data to a user. At step 129, the process ends.

These issues can be especially important to address for precious,difficult to collect, or low-abundance (e.g., less than 100 ng ofnucleic acid or samples containing a low abundance of undamaged oruncrosslinked nucleic acids) samples. For such samples, currentprotocols may lack repeatability, introduce loss of sample material,introduce bias for short or long nucleic acid targets, introduce biastowards sequence of nucleic acid targets, and/or lack repeatability.Such protocols may also lack compatibility with process automation ordownstream analyses. Current protocols for nucleic acid preparation caninclude liquid phase extraction (LPE) such as phenol-chloroformextraction or Trizol extraction, and solid phase extraction (SPE). SPEtype approaches can use structures including packed beads, monolithicporous structures, and/or magnetic beads. In some cases, LPE and SPEtype approaches can lead to mechanical shearing during processing whichcan cause fragmentation and/or reduce the yield of long or highmolecular weight nucleic acids.

The isotachophoresis methods and devices provided herein are especiallywell-suited to performing extraction of nucleic acids from lysates ofsolid or semi-solid tissues. Solid phase extraction (SPE) techniquestypically process lysates by pumping the entire lysate sample volumethrough a column in order to selectively adsorb nucleic acids onto thesurfaces of the column. Such pumping of a complex lysate, which maycomprise a liquid-particle mixture, through a porous column can resultin clogging or fouling of the column which can reduce the efficiency ofnucleic acid extraction. In contrast, the isotachophoresis methods anddevices described herein often do not involve pumping or “filtering” theentire lysate sample volume through a column. Instead, an electric fieldmay be applied to the lysate in order to cause the charged, solvatednucleic acids dispersed throughout the complex sample lysate to migratethrough and out of the continuous liquid phase of the sample. Nucleicacids may comprise a relatively high electrophoretic mobility magnituderelative to other solutes, debris, or contaminants in the sample lysate.Solutes in the sample may have a relatively low electrophoretic mobilityand be too low to focus into the isotachophoresis zone located at theinterface between the leading electrolytes and trailing electrolytes.Application of an electric field may cause the nucleic acids to migratewhile particles and/or other tissue debris (including for example celldebris, unlysed cells, or tissue which may connect cells to other cells)are left behind. The isotachophoresis methods and devices providedherein therefore can be well-suited to extract the charged, solvatednucleic acids out of the complex lysed solid tissue samples withouthaving to process the entire mixture through a column as in SPE.

As used herein, “particles” may refer to components of a sample mixtureor a sample lysate mixture which are a different phase than thecontinuous liquid phase of the sample (e.g., an aqueous solution).Particles may be non-liquid components of the sample mixture. Particlescan be, for example, suspended solid particles or colloidal bodiessuspended within a sample. Such particles can have a variety ofcharacteristic length scales ranging from about 1 nanometer (nm) toabout 1 millimeter (mm). In some instances, particles may not besingle-celled organisms or cells.

The isotachophoresis methods and devices provided herein may provide forreduced rates of strain as the sample moves through the channel comparedto typical SPE methods. In some cases, the methods and devices providedherein have rates of strain of less than about 250 s⁻¹, 500 s⁻¹, 750s⁻¹, 1000 s⁻¹, 2000 s⁻¹, 3000 s⁻¹, 4000 s⁻¹, 5000 s⁻¹, 6000 s⁻¹, 7000s⁻¹, 8000 s⁻¹, 9000 s⁻¹, or 10,000 s¹. In some cases, the methods anddevices provided herein have rates of strain of more than about 250 s⁻¹,500 s⁻¹, 750 s⁻¹, 1000 s⁻¹, 2000 s⁻¹, 3000 s⁻¹, 4000 s⁻¹, 5000 s⁻¹, 6000s⁻¹, 7000 s⁻¹, 8000 s⁻¹, 9000 s⁻¹, or 10,000 s⁻¹. In some cases, themethods provided herein may be performed without centrifugation.

Isotachophoresis Chemistry and Operation

FIG. 2A shows an exemplary schematic of an isotachophoresis (ITP)process purifying nucleic acid. A sample 201, for example a lysed solidtissue sample, comprising nucleic acids (DNA and RNA) 202 andcontaminants 203 is loaded with trailing electrolytes (TE) 204 into anisotachophoresis channel 200 containing leading electrolytes (LE) 205.Under the influence of an electric field 220 applied to theisotachophoresis channel 210, the nucleic acids 212 migrate away fromthe contaminants 213. The electric field also causes the trailingelectrolytes 214 to migrate through the channel in a position that isgenerally behind the nucleic acids, and causes the leading electrolytes215 to migrate through the channel generally ahead of the nucleic acids.The magnitude of the effective mobility of the leading electrolytes isgreater than the magnitude of the effective mobility of the nucleicacids, which in turn is greater than the magnitude of the effectivemobility of the trailing electrolytes, which is greater than themagnitude of the effective mobility of the contaminants.

FIG. 2B shows an exemplary schematic of a process to de-crosslinknucleic acids while separating de-crosslinked nucleic acids fromcrosslinked nucleic acids and contaminants (e.g., paraffin) usingisotachophoresis (ITP) on a fluidic device. In some instances, thecontaminants may comprise the crosslinked nucleic acids. Aparaffin-embedded sample is loaded onto the fluidic device in analkaline buffer and incubated for 10-30 minutes at about pH 10 and atemperature from about 50° C. to about 80° C. for tissue lysis andinitial deparaffinization. Incubation may occur prior to or whileapplying an electric field to perform isotachophoresis. Alternatively,the sample can be loaded in a leading electrolyte buffer. Afterincubation, at a first time point 240, the sample comprising crosslinkednucleic acids 236 and paraffin 237 is located in an ITP channel withtrailing electrolytes 232. Ahead in the ITP channel, in a leadingelectrolyte (LE) zone 238 are leading electrolytes 231 and Proteinase Kenzymes 233. At a second time point 250, at 50° C., ITP-driven pHquenching reduces the pH, and Proteinase K enzymes are contacting andde-crosslinking the crosslinked nucleic acids, producing non-crosslinkednucleic acids 235 which focus at in the ITP zone 239 between thetrailing electrolytes and leading electrolytes. Reduction of pH (e.g. toa range from about 10-12 to about 7 (or from about 6.5 to about 8.5))can provide an environment appropriate for enzymatic activity andimproved chemical stability of nucleic acids. At a third time point 260the Proteinase K has de-crosslinked more nucleic acids, resulting infree protein 234, and the de-crosslinked nucleic acids have furthermigrated upstream from the paraffin, free protein, and othercontaminants. The operation of such a process can be conductedautomatically by the fluidic device or by a benchtop system.

In some cases, the sample may be loaded in a sample buffer comprising aconcentration of leading electrolytes 205, 231 that differs from theconcentration of leading electrolytes 205, 231 used to performisotachophoresis. In some cases, the sample may be loaded in a samplebuffer comprising a second leading electrolyte which differs from theleading electrolyte 215. The second leading electrolyte can have aneffective mobility magnitude greater than the magnitude the effectivemobility of the nucleic acid. The second leading electrolyte can have aneffective mobility magnitude less than the effective mobility magnitudeof the leading electrolyte 215.

In some cases, a pH of the sample may be quenched by conductingisotachophoresis. In some instances, the pH of the sample may bequenched within a range of about 6.5 to about 8.5, for example about 7or 7.5.

Various leading electrolytes and trailing electrolytes can be used toconduct ITP. Leading electrolytes can be selected to have a greatereffective mobility magnitude than the extraction target (e.g., nucleicacids), and trailing electrolytes can be selected to have a lessereffective mobility magnitude than the extraction target. Leading and/ortrailing electrolytes can be present at a concentration from about 10 mMto about 200 mM. Leading and/or trailing electrolytes can be present ata concentration of about 10 mM, 20 mM, 30 mM, 40 mM, 50 mM, 60 mM, 70mM, 80 mM, 90 mM, 100 mM, 110 mM, 120 mM, 130 mM, 140 mM, 150 mM, 160mM, 170 mM, 180 mM, 190 mM, or 200 mM. Leading and/or trailingelectrolytes can be present at a concentration of at least about 10 mM,20 mM, 30 mM, 40 mM, 50 mM, 60 mM, 70 mM, 80 mM, 90 mM, 100 mM, 110 mM,120 mM, 130 mM, 140 mM, 150 mM, 160 mM, 170 mM, 180 mM, 190 mM, or 200mM. Leading and/or trailing electrolytes can be present at aconcentration of at most about 10 mM, 20 mM, 30 mM, 40 mM, 50 mM, 60 mM,70 mM, 80 mM, 90 mM, 100 mM, 110 mM, 120 mM, 130 mM, 140 mM, 150 mM, 160mM, 170 mM, 180 mM, 190 mM, or 200 mM. Leading electrolytes used in aparticular instance of ITP can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,or more different ion species. Trailing electrolytes used in aparticular instance of ITP can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,or more different ion species. Different species of ions in the leadingelectrolytes and/or trailing electrolytes can be present at differentconcentrations. Different concentrations of ions, such as within thetrailing electrolytes or the leading electrolytes, can be selected tomanipulate the size of a spacing zone. The spacing zone can be used tofurther separate one type of target from another, such as separatingdecrosslinked from protein crosslinked nucleic acids.

The trailing electrolytes can comprise a mixture of ions with differentmagnitudes of effective mobilities. Use of a first trailing electrolyteion with a first effective mobility magnitude and a second trailingelectrolyte ion with a second effective mobility magnitude lower thanthat of the first ion can be used to separate non-crosslinked nucleicacids from protein crosslinked nucleic acids, while separating both (orat least the decrosslinked nucleic acids) from contaminants. In such acase, the non-crosslinked nucleic acids can have a greater effectivemobility magnitude than the first trailing electrolyte ions, which canhave a greater effective mobility magnitude than the crosslinked nucleicacids, which in turn can have a greater effective mobility magnitudethan the second trailing electrolyte ions, which in turn can have agreater effective mobility magnitude than the contaminants. For example,crosslinked and non-crosslinked nucleic acids can be enriched separatelyby conducting isotachophoresis using a leading electrolyte and twotrailing electrolytes, such as caproic acid as the first ion and HEPESas the second ion.

Electrolyte ions can also be selected based on acidity (e.g., pKa). Ionswith particular pKa can be selected, for example, to effect a pH changealong an ITP channel. Ions can also be selected for non-electrophoreticreasons, such as compatibility with downstream processes (e.g.,enzymatic processes such as PCR or next-generation sequencing librarypreparation). For example, caproic acid, MOPS, and HEPES can be selectedfor good downstream enzymatic compatibility.

Exemplary leading electrolyte ions include but are not limited tohydrochloric acid, acetic acid, 2-chloroisocrotonic acid, salicylicacid, chlorocrotonic acid, nicotinic acid, gallic acid, trichlorolacticacid, butyric acid, sulfanilic acid, benzoic acid, crotonic acid,trichloroacrylic acid, propionic acid, levulinic acid, sorbic acid,orotic acid, valeric acid, picric acid, 2-naphtalenesulfonic acid,saccharin, dinitrophenol, p-toluenesulfonic acid, aspartic acid,trimethylacrylic acid, isocaproic acid, caproic acid, octylsulfonicacid, nitrophenol, GABA, cacodylic acid, trimetylpyruvic acid,ethylmaleic acid, ethylfumaric acid, toluic acid, enanthylic acid,mandelic acid, cinnamic acid, cresol, glutamic acid, MES, isomersthereof, and combinations thereof.

Exemplary trailing electrolyte ions include but are not limited tocaprylic acid, gluconic acid, vanillic acid, decylsulfonic acid,aspirin, glucuronic acid, pelargonic acid, benzylasparatic acid,ascorbic acid, dodecylsulfonic acid, MOPS(3-(N-morpholino)propanesulfonic acid), dichlorophenol, caproic acid,capric acid, tyrosine, HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), isomers thereof,and combinations thereof.

Use of a mixture of different trailing electrolyte ions can be used toachieve mobility bracketed separations (e.g., separation ofnon-crosslinked nucleic acids from crosslinked nucleic acids fromcontaminants), compatibility with downstream assays, favorable surfaceenergy or contact angles between fluids and fluidic device materials,buffering capacity, and total ion solubility.

Isotachophoresis can quench the pH of a sample to neutral or aboutneutral. Ions affecting the local pH (e.g., sodium ions (Na+)) can bedisplaced from the sample zone during isotachophoresis, thereby shiftingthe pH in the sample zone toward neutral.

Isotachophoresis can be conducted at a range of voltages, currents, andfield strengths. For example, isotachophoresis can be conducted at avoltage from about 100 V and about 1500 V. Isotachophoresis can beconducted at a voltage of about 100 V, 200 V, 300 V, 400 V, 500 V, 600V, 700 V, 800 V, 900 V, 1000 V, 1100 V, 1200 V, 1300 V, 1400 V, or 15000V. Isotachophoresis can be conducted at a voltage of at least about 100V, 200 V, 300 V, 400 V, 500 V, 600 V, 700 V, 800 V, 900 V, 1000 V, 1100V, 1200 V, 1300 V, 1400 V, or 15000 V. Isotachophoresis can be conductedat a voltage of at most about 100 V, 200 V, 300 V, 400 V, 500 V, 600 V,700 V, 800 V, 900 V, 1000 V, 1100 V, 1200 V, 1300 V, 1400 V, or 15000 V.Isotachophoresis can be conducted at a current from about 10 nA to about10 mA. Isotachophoresis can be conducted at a current of about 10 nA, 20nA, 30 nA, 40 nA, 50 nA, 60 nA, 70 nA, 80 nA, 90 nA, 100 nA, 200 nA, 300nA, 400 nA, 500 nA, 600 nA, 700 nA, 800 nA, 900 nA, 1 mA, 2 mA, 3 mA, 4mA, 5 mA, 6 mA, 7 mA, 8 mA, 9 mA, or 10 mA. Isotachophoresis can beconducted at a current of at least about 10 nA, 20 nA, 30 nA, 40 nA, 50nA, 60 nA, 70 nA, 80 nA, 90 nA, 100 nA, 200 nA, 300 nA, 400 nA, 500 nA,600 nA, 700 nA, 800 nA, 900 nA, 1 mA, 2 mA, 3 mA, 4 mA, 5 mA, 6 mA, 7mA, 8 mA, 9 mA, or 10 mA. Isotachophoresis can be conducted at a currentof at most about 10 nA, 20 nA, 30 nA, 40 nA, 50 nA, 60 nA, 70 nA, 80 nA,90 nA, 100 nA, 200 nA, 300 nA, 400 nA, 500 nA, 600 nA, 700 nA, 800 nA,900 nA, 1 mA, 2 mA, 3 mA, 4 mA, 5 mA, 6 mA, 7 mA, 8 mA, 9 mA, or 10 mA.Isotachophoresis can be conducted at a field strength of from about 10V/cm to about 100 V/cm. Isotachophoresis can be conducted at a fieldstrength of about 10 V/cm, 15 V/cm, 20 V/cm, 25 V/cm, 30 V/cm, 35 V/cm,40 V/cm, 45 V/cm, 50 V/cm, 55 V/cm, 60 V/cm, 65 V/cm, 70 V/cm, 75 V/cm,80 V/cm, 85 V/cm, 90 V/cm, 95 V/cm, or 100 V/cm. Isotachophoresis can beconducted at a field strength of at least about 10 V/cm, 15 V/cm, 20V/cm, 25 V/cm, 30 V/cm, 35 V/cm, 40 V/cm, 45 V/cm, 50 V/cm, 55 V/cm, 60V/cm, 65 V/cm, 70 V/cm, 75 V/cm, 80 V/cm, 85 V/cm, 90 V/cm, 95 V/cm, or100 V/cm. Isotachophoresis can be conducted at a field strength of atmost about 10 V/cm, 15 V/cm, 20 V/cm, 25 V/cm, 30 V/cm, 35 V/cm, 40V/cm, 45 V/cm, 50 V/cm, 55 V/cm, 60 V/cm, 65 V/cm, 70 V/cm, 75 V/cm, 80V/cm, 85 V/cm, 90 V/cm, 95 V/cm, or 100 V/cm.

Isotachophoresis can be used to concentrate nucleic acids in a sample.The concentration of nucleic acids in a sample can be increased afterisotachophoresis by at least about 2-fold, 5-fold, 10-fold, 100-fold,1,000-fold, 10,000-fold, 100,000-fold, 1,000,000-fold, 10,000,000-fold,100,000,000-fold, or 1,000,000,000-fold. The operation time forconcentration of nucleic acids with isotachophoresis can be less than orequal to about 5 hours, 4.5 hours, 4 hours, 3.5 hours, 3 hours, 2.5hours, 2 hours, 1.5 hours, 1 hours, 50 minutes, 40 minutes, 30 minutes,20 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5minutes, 4 minutes, 3 minutes, 2 minutes, 1 minute, 45 seconds, 30seconds, 20 seconds 10 seconds, or 1 second. In some cases,isotachophoresis can be used to increase the concentration of nucleicacids in a sample by 1,000,000-fold in less than or equal to about 2minutes. In some cases (e.g., from a sample of 25 μL blood lysate),isotachophoresis can be used to increase the concentration of nucleicacids in a sample by 100,000-fold in less than or equal to about 5minutes.

Techniques of the present disclosure can be used to reduce theconcentration of crosslinked nucleic acids in a sample. Theconcentration of crosslinked nucleic acids in a sample can be reducedafter isotachophoresis by at least about 2-fold, 5-fold, 10-fold,100-fold, 1,000-fold, 10,000-fold, 100,000-fold, 1,000,000-fold,10,000,000-fold, 100,000,000-fold, or 1,000,000,000-fold.Isotachophoresis can be used to reduce the concentration of acontaminant in a sample. The concentration of contaminants in a samplecan be reduced after isotachophoresis by at least about 2-fold, 5-fold,10-fold, 100-fold, 1,000-fold, 10,000-fold, 100,000-fold,1,000,000-fold, 10,000,000-fold, 100,000,000-fold, or1,000,000,000-fold.

Nucleic acid samples can contain from about 0.1 picograms (pg) to about25 micrograms (μg). For example, nucleic acid samples can contain fromabout 5 pg to about 5 μg. Nucleic acid samples can contain about 0.1 pg,0.2 pg, 0.3 pg, 0.4 pg, 0.5 pg, 0.6 pg, 0.7 pg, 0.8 pg, 0.9 pg, 1 pg, 2pg, 3 pg, 4 pg, 5 pg, 6 pg, 7 pg, 8 pg, 9 pg, 10 pg, 20 pg, 30 pg, 40pg, 50 pg, 60 pg, 70 pg, 80 pg, 90 pg, 100 pg, 200 pg, 300 pg, 400 pg,500 pg, 600 pg, 700 pg, 800 pg, 900 pg, 1 nanogram (ng), 2 ng, 3 ng, 4ng, 5 ng, 6 ng, 7 ng, 8 ng, 9 ng, 10 ng, 20 ng, 30 ng, 40 ng, 50 ng, 60ng, 70 ng, 80 ng, 90 ng, 100 ng, 200 ng, 300 ng, 400 ng, 500 ng, 600 ng,700 ng, 800 ng, 900 ng, 1 μg, 2 μg, 3 μg, 4 μg, 5 μg, 6 μg, 7 μg, 8 μg,9 μg, 10 μg, 11 μg, 12 μg, 13 μg, 14 μg, 15 μg, 16 μg, 17 μg, 18 μg, 19μg, 20 μg, 21 μg, 22 μg, 23 μg, 24 μg, or 25 pg.

Nucleic acid samples can comprise deoxyribonucleic acids (DNA),single-stranded DNA, double-stranded DNA, genomic DNA, complementaryDNA, ribonucleic acids (RNA), ribosomal RNA, transfer RNA, messengerRNA, micro RNA, or the like, or any combination thereof. Nucleic acidsamples can comprise a length of at least about 0.5, 1, 2, 5, 10, 20,30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, or500 kB or more. Techniques of the present disclosure can be used toextract different sample types in different channels of a fluidicdevice. For example, different channels may be used to extract nucleicacids of different lengths and/or different types.

In some instances, a characteristic of a nucleic acid sample may becompared to one or more nucleic acids from another sample. Thecharacteristic may for example be an expression level, a nucleic acidsequence, a molecular weight, nucleic acid integrity, nucleic-acidstranded-ness, or nucleic acid purity.

Nucleic acid samples can be of a particular quality before and/or afterextraction or other processing. Nucleic acid quality can be assessed byvarious metrics, including but not limited to RNA integrity number(RIN), DNA integrity number (DIN), size distribution (e.g., usingelectrophoresis), and ability to be amplified (e.g., by PCR) orotherwise enzymatically processed (e.g. fragmentation, ligation,a-tailing, or hybridization for next generation sequencing librarypreparation). Techniques of the present disclosure can be used toextract or process nucleic acids and provide extracted or processednucleic acids with a RIN of at least about 1.0, 1.1, 1.2, 1.3, 1.4, 1.5,1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9,3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3,4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7,5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1,7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5,8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or10.0. Techniques of the present disclosure can be used to extract orprocess nucleic acids and provide extracted or processed nucleic acidswith a RIN of at most about 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8,1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2,3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6,4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0,6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4,7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8,8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or 10.0.Techniques of the present disclosure can be used to extract or processnucleic acids and provide extracted or processed nucleic acids with aDIN of at least about 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9,2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3,3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7,4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1,6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5,7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9,9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or 10.0. Techniques ofthe present disclosure can be used to extract or process nucleic acidsand provide extracted or processed nucleic acids with a DIN of at mostabout 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2,2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6,3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0,5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4,6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8,7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2,9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or 10.0. Techniques of the presentdisclosure can be used to extract or process nucleic acids and provideextracted or processed nucleic acids such that at least 10%, 20%, 30%,40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 99.99%of the mass of the nucleic acids of the sample has a molecular weight ofat least about 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,150, 200, 250, 300, 350, 400, 450, or 500 kB or more. In some cases,about 90% to about 100% of the mass of the processed nucleic acids arefrom about 10 to about 1000 bp, from about 200 to about 2000 bp, or fromabout 200-5000 bp.

Isotachophoresis can be used to extract nucleic acids at an extractionefficiency or yield, characterized as the percent yield of nucleic acidfrom a given starting amount of nucleic acid. Techniques of the presentdisclosure can provide extracted nucleic acids at a yield of at leastabout 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.9%. Techniques of thepresent disclosure can provide high yields even for low input amountsnucleic acid, including less than or equal to about 10⁴ nanograms (ng),10³ ng, 10² ng, 10¹ ng, 10° ng, 10⁴ ng, or 10⁻² ng. FIG. 3, for example,shows exemplary nucleic acid yields from a range of different inputamounts and sources of nucleic acid. High yield and/or low loss ofnucleic acids can be important for next generation sequencing librarypreparations. Recovery of nucleic acids can be at or near 100%.

Techniques of the present disclosure can extract nucleic acids with lowor no sequence bias. That is, the sequence composition of the extractedand purified nucleic acids (e.g., ratio of GC-rich nucleic acids toAT-rich nucleic acids) can be similar to or the same as the sequencecomposition of the input nucleic acids (see, e.g., FIG. 4A). Thedifference in sequence composition of the extracted nucleic acids fromthe sequence composition of the input nucleic acids can be less than orequal to about 20%, 15%, 10%, 5%, 4%, 3%, 2%, or 1%.

Techniques of the present disclosure can extract nucleic acids with lowor no length bias. That is, the length distribution of the extractednucleic acids (e.g., the proportions of nucleic acids of differentsizes) can be similar to or the same as the length distribution of theinput nucleic acids (see, e.g., FIG. 4B). The difference in lengthdistribution of the extracted nucleic acids from the length distributionof the input nucleic acids can be less than or equal to about 20%, 15%,10%, 5%, 4%, 3%, 2%, or 1%. For example, short nucleic acids (e.g.,about 10 to about 300 bp), long nucleic acids (e.g., about 10 kB, 20 kB,30 kB, 40 kB, 50 kB, 60 kB, 70 kB, 80 kB, 90 kB, 100 kB, or greater), orboth short and long nucleic acids can be extracted with reduced drop outor bias. Solid phase columns can, in some cases, lose up to 100% ofshort and/or long nucleic acid material. Techniques of the currentdisclosure can recover nucleotides from single base to hundreds ofkilobases in size. Techniques of the present disclosure can recover atleast about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95%, 96%,97%, 98%, 99%, 99.9%, or 100% of short and/or long nucleic acids presentin the sample.

Techniques of the present disclosure can result in the removal ofcontaminants from the sample. Contaminants can include but are notlimited to embedding material, cell debris, extracellular matrixcomponents, tissue debris, embedding debris, lipids, carbohydrates,enzymes, ligation by-products, primers, unbound probes or ligators,divalent metals, detergents, preservatives, fixatives, anti-coagulants,collagen fibers, and PCR inhibitors. Contaminants can originate from thetissue or cells of the sample, from preservatives or embedding materialsused on the sample, or from previous preparations, reactions, or assaysperformed on the sample. For example, enzymes such as restrictionnucleases can be used to prepare DNA for a fingerprinting assay, andsubsequent to digestion (e.g., DNase digestion), DNA can be separatedfrom the enzyme.

Samples

The techniques of the present disclosure can be used to processdifferent sample types, including but not limited to biological samples,solid tissue, biopsies, tissue biopsies, liquid biopsies, organs,tumors, fresh tissue, solid organs, preserved tissue (e.g., FFPE),dissected FFPE, fresh frozen tissue, fixed samples, fixed tissue,embedded samples, lysed samples, un-lysed samples, samples comprisingconnections between cells (e.g. gap junctions, tight junctions, adherentjunctions), samples comprising lysed solid tissue and nucleic acids,multiphasic samples, inhomogeneous liquids or solutions (such as tissue,whole blood, or unlysed cell suspensions), biological samples comprisinggenomic DNA, lysed and un-lysed whole blood, plasma and serum, buccalswabs, dried blood spots and other forensic samples, fresh or freshfrozen (FF) tissues, cultured or harvested cells (lysed and un-lysed)from blood or tissues, fixed cells, stool, and bodily fluids (e.g.,saliva, urine), or any combination thereof. Non-limiting examples ofsolid organs include liver, pancreas, brain, heart, gall bladder, colon,lung and reproductive organs. Samples can include cellular and cell-freenucleic acids, for both eukaryotic and prokaryotic organisms. Fixedsamples can be chemically fixed or physically fixed (e.g., heating orfreezing). For example, samples can be chemically fixed with a chemicalfixative such as formalin, neutral buffered formalin (NBF),formaldehyde, paraformaldehyde, glutaraldehyde, glyoxal, mercuricchloride, zinc salts, Bouin's fluid, alcohol-formalin-acetic acid (AFAor FAA), citrate-acetone-formalin (CAF), acetone, methanol, ethanol,Clarke's fluid, Carnoy's fluid, or Puchtler's methacarn. Embeddedsamples can be embedded in materials including but not limited to wax(e.g., paraffin), agar, gelatin, or plastic resins. Formalin-fixedparaffin-embedded (FFPE) samples can be processed using techniques ofthe present disclosure. Samples can comprise buccal swabs, blood spots,and other forensic samples. Samples can comprise clinical samples, fineneedle aspirates, biopsies, whole blood, lysed blood, serum, plasma,urine, cell culture lysate or freshly harvested cell (e.g., blood cell,dissociated fresh tissue, stem cell) lysate, blood cells, circulatingcells (e.g., circulating tumor cells (CTCs)), nucleic acids from bloodor other bodily fluid, and other sample categories. Cell-free nucleicacids (e.g., cfDNA or cfRNA) can be recovered, such as from wholeun-lysed blood, using techniques of the present disclosure; often thecell-free nucleic acids are circulating cell-free nucleic acids. Samplescan be from a variety of sources, including but not limited to normaltissue, benign neoplasms, malignant neoplasms, stem cells, human tissue,animal tissue, plant tissue, bacteria, viruses, and environmentalsources (e.g., water). Human or animal tissues can include but are notlimited to epithelial tissue, connective tissue (e.g., blood, bone),muscle tissue (e.g., smooth muscle, skeletal muscle, cardiac muscle),and nervous tissue (e.g., brain, spinal cord).

Samples can comprise one or more particles in suspension. The one ormore particles may range from colloidal size to visible. The one or moreparticles can have a size of at least about 1 nanometer (nm), 10 nm, 20nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 150 nm, 200nm, 250 nm, 300 nm, 350 nm, 400 nm, 450 nm, 500 nm, 600 nm, 700 nm, 800nm, 900 nm, 950 nm, 1 micrometer (ρm), 10 μm, 20 μm, 30 μm, 40 μm, 50μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 150 μm, 175 μm, 200 μm, 225 μm,250 μm, 275 μm, 300 μm, 350 μm, 400 μm, 450 μm, 500 μm, 550 μm, 600 μm,650 μm, 700 μm, 750 μm, 800 μm, 850 μm, 900 μm, 950 μm, or 1 millimeter(mm). The one or more particles can have a size of at most about 1nanometer (nm), 10 nm, 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm,90 nm, 100 nm, 150 nm, 200 nm, 250 nm, 300 nm, 350 nm, 400 nm, 450 nm,500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 950 nm, 1 micrometer (μm), 10μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 150μm, 175 μm, 200 μm, 225 μm, 250 μm, 275 μm, 300 μm, 350 μm, 400 μm, 450μm, 500 μm, 550 μm, 600 μm, 650 μm, 700 μm, 750 μm, 800 μm, 850 μm, 900μm, 950 μm, or 1 millimeter (mm). The one or more particles can be thesame size or different sizes. A sample may for example comprise aplurality of particles ranging in size from 1 nm to 500 μm.

Samples of various volumes can be processed on a fluidic device (e.g.,to extract and purify nucleic acids). For example, a sample volume (withor without buffer) can be at least about 1 nanoliter (nL), 10 nL, 20 nL,50 nL, 100 nL, 200 nL, 500 nL, 1 microliter (4), 10 μL, 20 μL, 30 μL, 40μL, 50 μL, 60 μL, 70 μL, 80 μL, 90 μL, 100 μL, 150 μL, 175 μL, 200 μL,225 μL, 250 μL, 275 μL, 300 μL, 350 μL, 400 μL, 450 μL, 500 μL, 600 μL,700 μL, 800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL,7 mL, 8 mL, 9 mL, or 10 mL. A sample volume (with or without buffer) canbe at most about 1 nanoliter (nL), 10 nL, 20 nL, 50 nL, 100 nL, 200 nL,500 nL, 1 microliter (4), 10 μL, 20 μL, 30 μL, 40 μL, 50 μL, 60 μL, 70μL, 80 μL, 90 μL, 100 μL, 200 μL, 300 μL, 400 μL, 500 μL, 600 μL, 700μL, 800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7mL, 8 mL, 9 mL, or 10 mL. In some cases, a sample volume can be fromabout 1 nL to about 10 nL. A sample volume (with or without buffer) canbe at least about 1 nanoliter (nL), 10 nL, 20 nL, 50 nL, 100 nL, 200 nL,500 nL, 1 microliter (4), 10 μL, 20 μL, 30 μL, 40 μL, 50 μL, 60 μL, 70μL, 80 μL, 90 μL, 100 μL, 200 μL, 300 μL, 400 4, 500 μL, 600 μL, 700 μL,800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8mL, 9 mL, or 10 mL. In some cases, a sample volume can be from about 1nL to about 10 nL.

Samples with different numbers of cells can be processed on a fluidicdevice (e.g., to extract and purify nucleic acids). For example, asample can contain less than or equal to about 20,000 cells, 15,000cells, 10,000 cells, 9,000 cells, 8,000 cells, 7,000 cells, 6,000 cells,5,000 cells, 4,500 cells, 4,000 cells, 3,500 cells, 3,000 cells, 2,500cells, 2,000 cells, 1,500 cells, 1,000 cells, 900 cells, 800 cells, 700cells, 600 cells, 500 cells, 400 cells, 300 cells, 200 cells, 100 cells,90 cells, 80 cells, 70 cells, 60 cells, 50 cells, 40 cells, 30 cells, 20cells, 10 cells, 5 cells, 2 cells, or 1 cell. In some cases, a samplecontains at least about 10,000,000 cells, 5,000,000 cells, 1,000,000cells, 500,000 cells, 100,000 cells, 50,000 cells, 20,000 cells, 15,000cells, 10,000 cells, 9,000 cells, 8,000 cells, 7,000 cells, 6,000 cells,5,000 cells, 4,500 cells, 4,000 cells, 3,500 cells, 3,000 cells, 2,500cells, 2,000 cells, 1,500 cells, 1,000 cells, 900 cells, 800 cells, 700cells, 600 cells, 500 cells, 400 cells, 300 cells, 200 cells, or 100cells.

Samples of different masses can be processed on a fluidic device (e.g.,to extract and purify nucleic acids). For example, a sample can containfrom about 0.001 milligrams (mg) and about 10 mg of tissue. A sample cancontain at most about 0.001 mg, 0.002 mg, 0.003 mg, 0.004 mg, 0.005 mg,0.006 mg, 0.007 mg, 0.008 mg, 0.009 mg, 0.01 mg, 0.02 mg, 0.03 mg, 0.04mg, 0.05 mg, 0.06 mg, 0.07 mg, 0.08 mg, 0.09 mg, 0.1 mg, 0.2 mg, 0.3 mg,0.4 mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, 1 mg, 2 mg, 3 mg, 4 mg,5 mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg of tissue. A sample can containat least about 0.001 mg, 0.002 mg, 0.003 mg, 0.004 mg, 0.005 mg, 0.006mg, 0.007 mg, 0.008 mg, 0.009 mg, 0.01 mg, 0.02 mg, 0.03 mg, 0.04 mg,0.05 mg, 0.06 mg, 0.07 mg, 0.08 mg, 0.09 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, 1 mg, 2 mg, 3 mg, 4 mg, 5mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg of tissue. A sample can containabout 0.001 mg, 0.002 mg, 0.003 mg, 0.004 mg, 0.005 mg, 0.006 mg, 0.007mg, 0.008 mg, 0.009 mg, 0.01 mg, 0.02 mg, 0.03 mg, 0.04 mg, 0.05 mg,0.06 mg, 0.07 mg, 0.08 mg, 0.09 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4 mg, 0.5mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg,7 mg, 8 mg, 9 mg, or 10 mg of tissue.

Samples with different amounts of nucleic acid can be processed on afluidic device (e.g., to extract and purify nucleic acids). For example,samples can contain less than or equal to about 1 microgram (1 μg), 100nanograms (ng), 10 ng, 1 ng, 100 picograms (pg), 10 pg, or 1 pg ofnucleic acid. In some cases, samples can contain greater than or equalto about 1 microgram (1 μg), 100 nanograms (ng), 10 ng, 1 ng, 100picograms (pg), 10 pg, or 1 pg of nucleic acid.

Samples can be loaded in a buffer comprising trailing electrolyte orleading electrolyte. Samples can be loaded in a buffer comprising asecond leading electrolyte which differs from the leading electrolyteused to perform ITP. Samples can be loaded in a buffer, such as anaqueous alkaline or a neutral aqueous buffer. Exemplary alkalinesolutions or buffers (e.g., for DNA extraction) can comprise 30-120 mMNaOH (in some cases, 40-80 mM NaOH) at a pH of about 10-13 (in somecases, with at least one additional component). In some instances, whenthe sample is lysed via treatment with an alkaline solution or bufferprior to loading onto the chip, the lysed sample may subsequently bequenched by adding an acidic solution or buffer to bring the pH of thelysed sample within a range of about 7.5 to about 8.5 prior toperforming isotachophoresis. Exemplary aqueous buffers (e.g., for DNA orRNA extraction) can comprise 2-150 mM Tris-HCl (at a pH of about 7 toabout 8) or BisTris-HCl at a pH of about 5.8 to about 7.3, with at leastone additional component. Additional components used in buffers caninclude non-ionic surfactants or detergents, ionic or zwitter-ionicsurfactants or detergents, chaotropic agents, disulfide bond reducingagents, proteases, nucleases, and other additives or components thatdigest, denature, disrupt, or degrade for the purpose of extracting,purifying, enriching, or otherwise isolating nucleic acids.

Non-ionic surfactants or detergents can include but are not limited tosurfactants from the following classes: octylphenol ethoxylate,polysorbate, poloxamer, or polyoxyethylene. Octylphenol ethoxylatesurfactants can include but are not limited to branched octylphenoxypolyethoxy ethanol (IGEPAL CA-630), t-octylphenoxypolyethoxyethanol(Triton™ X-100), or other polyethylene oxide chains with an aromatichydrocarbon lipophilic or hydrophobic group. Polysorbate surfactants caninclude but are not limited to polyethylene glycol sorbitan monolaurate(Tween® 20), polyethylene glycol sorbitan monooleate (Tween® 80), orsorbitan monooleate (Span® 80). Poloxamer surfactants (i.e. blockcopolymers based on ethylene oxide and propylene oxide) can include butare not limited to polyoxyethylene-polyoxypropylene block copolymer(Pluronic® F-68) or polyethylene-polypropylene glycol block copolymer(Pluronic® F-127). Polyoxyethylene surfacts can include but are notlimited to nonyl phenoxypolyethoxylethanol (NP-40).

Non-ionic surfactants or detergents can include but are not limited toIGEPAL® (e.g., IGEPAL® CA-630), Triton™ X-100, Tween® 20, Tween® 80,NP-40, other block copolymers including Pluronic® (e.g., F-68 or F-127),Span® 80, and pegylated polymers or copolymers. Non-ionic surfactants ordetergents can be used to reduce or prevent biological moleculeadsorption to channel walls, or to control wetting and/or surfacetension properties of fluids to control loading of sample into fluidicdevices. Non-ionic surfactants or detergents can be present atconcentrations from about 0.0005-5% v/v or w/v. For example, IGEPALCA-630 can be used at about 0.05-0.5% v/v. Ionic surfactants ordetergents can include but are not limited to sodium dodecyl sulfate(e.g., at 0.01-2% w/v), sodium dodecylbenzenesulfonate (e.g., at 0.01-2%w/v), sodium cholesteryl sulfate (e.g., at 0.01%-2% w/v), and sodiumdeoxycholate (e.g., at about 10-1000 mM). Chaotropic agents can includebut are not limited to urea (e.g., at about 0.5-9.5 M, or in some cases,5-9.5 M) thiourea, butanol ethanol, guanidinium chloride, lithiumperchlorate, lithium acetate, lithium chloride, magnesium chloride,phenol, and propanol. For example, 7.0 M urea and 2.0 M thiourea can beused in a 5-50 mM Tris-HCl (in some cases, 10-20 mM Tris-HCl) bufferedsolution for either RNA or DNA extractions, or for total nucleic acidextractions. The ratio of urea to thiourea can be at least about 1:1,1.5:1, 2:1, 2.5:1, 3:1, 3.5:1, 4:1, 4.5:1, 5:1, 6:1, 6.5:1, 7:1, 7.5:1,or 8:1. Disulfide bond reducing agents can include but are not limitedto DTT (e.g. at about 0.1-40 mM, or in some cases about 10 mM) andbetamercaptoethanol (e.g., at about 0.5-2%, or in some cases about 1%).Proteases can include but are not limited to Proteinase K, proteases,endoproteinases (e.g., trypsin, LysC, GluC, AspN), peptidases, pepsin,and papain. Nucleases can include but are not limited to non-specificnucleic acid digestion enzymes such as DNases including DNase I (e.g.,to prepare DNA-free RNA extractions) and RNase, such as RNase A, RNaseT, or combinations thereof (e.g., to prepare RNA-free DNA extractions).Nucleases can also include specific nucleic acid digestion enzymes(e.g., restriction enzymes) which can cut at specific nucleic acidsequences and can produce predictable fragment sizes and fragment sizedistributions. In some cases, one or more methods or processes providedherein are performed without use of a nuclease, without use of a DNAse,or without use of an RNAase. For example, the methods provided hereininclude extraction of RNA without use of DNAase.

Restriction enzymes can include but are not limited to Type 1 throughType V restriction enzymes, BamHI, EcoP151, EcoRI, EcoRII, EcoRV,HaeIII, HgaI, HindIII, HinFI, KpnI, NotI, PstI, PvuII, SacI, SalI, SmaI,SpeI, SphI, XbaI, and StuI. Nucleases can be used at concentrationsincluding 50-400 pg/mL. Nuclease digestions can be performed attemperatures including from about 20° C. to about 37° C. Other nucleicacid modifying enzymes can be used, such as transposases, ligases,polymerases, and phosphatases. Other protein or polynucleotide digestionor degradation agents can be used, such as lysozymes.

Prior to loading onto a fluidic device, samples can be subjected tovarious degrees of pre-processing. In some cases, a sample can be simplyloaded into buffer prior to loading onto a fluidic device, and any othernecessary or desired sample preparation steps can be conducted on thedevice. In other cases, sample can be added to a sample reservoir thatis prefilled with a processing fluid such as a solution or buffer. Inother cases, a sample can be subjected to removal of embedding material,tissue disruption, cell lysis, or digestion prior to loading on afluidic device. In one example, a sample is deparaffinized prior toloading onto a fluidic device, and de-crosslinking of nucleic acids isconducted on the fluidic device. In another example, a sample isdeparaffinized, disrupted, and lysed prior to loading onto a fluiddevice, and, optionally, de-crosslinking of nucleic acids is conductedon the fluidic device. In another example, a sample is deparaffinizedprior to loading onto a fluidic device, and tissue disruption and celllysis are conducted on the fluidic device. In another example, a sampleis loaded onto a fluidic device, and deparaffinization, tissuedisruption, cell lysis, and de-crosslinking of nucleic acids are allconducted on the fluidic device. Sample preparation steps are discussedfurther in this disclosure.

Sample Preparation

Samples can be prepared prior to isotachophoresis. Sample preparationcan involve steps including but not limited to removal of embeddingmaterial, tissue disruption, cell lysis, digestion of proteins, removalof nucleic acid crosslinking, isothermal enzymatic process, enzymaticamplification, enzymatic digestion, disruption of cell-cell junctions,disruption of extracellular matrix, disruption of connective tissue, andcombinations thereof. Sample preparation can involve techniques such aspolymerase chain reaction (PCR) or other nucleic acid amplification,isolation or purification of material (e.g., cells, nucleic acids) ofinterest, probe hybridization, and antibody hybridization (e.g.,hybridization of antibodies to nucleosomes). In some cases, samples canbe prepared by isolating a portion of material from cells from thesample for further analysis. For example, circulating tumor cells can beisolated from a heterogenous population of cells using a cell sortingdevices such as a flow cytometer or magnetized column. In anotherexample, peripheral blood lymphocytes (PBLs) or peripheral bloodmononuclear cells (PBMCs) can be isolated from a blood sample. Samplepreparation can be conducted on-device or off-device. In some cases,some sample preparation steps are conducted off-device, and then thesample is loaded onto a fluidic device where additional samplepreparation steps are conducted.

Biological material (e.g., cells, tissue, nucleic acids) in an embeddedsample can be removed from the embedding material. For example, aparaffin-embedded sample can be deparaffinized. Removal of embeddingmaterial can be conducted using techniques including but not limited toheat treatment, chemical treatment (e.g., acid or base), enzymatictreatment, and combinations thereof. Deparaffinization can be performedby chemical treatment of a sample, by heat-treating a sample, byenzymatic treatment of a sample, or by other methods. For example,deparaffinization can be conducted at an elevated temperature (e.g. fromabout 50° C. to about 80° C.) in the presence of a neutral buffer orsomewhat acidic buffer (e.g., down to pH about 5.5) buffer or somewhatbasic (up to pH about 9) or alkaline solution (e.g., pH from about 12 toabout 13). Removal of embedding material can be conducted off-device oron-device. In one example, an embedded sample can be incubated at anelevated temperature in a vessel and subsequently loaded onto a fluidicdevice. In another example, an embedded sample can be loaded onto afluidic device and incubated at an elevated temperature on the device,for example in the channel or a reservoir.

Removal of embedding material can be conducted by heat treatment.Incubation for removal of embedding material can be conducted at atemperature of at least about 35° C., 37° C., 40° C., 45° C., 50° C.,55° C., 60° C., 65° C., 70° C., 75° C., 80° C., 85° C., 90° C., 95° C.,96° C., 97° C., 98° C., 99° C., 99.5° C., or 100° C. Incubation forremoval of embedding material can be conducted at a temperature fromabout 40° C. to about 80° C., from about 50° C. to about 80° C., fromabout 50° C. to about 99.9° C., or about 95 to about 99.5° C. Incubationfor removal of embedding material can be conducted for a duration of atleast about 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6minutes, 7 minutes, 8 minutes, 9 minutes, 10 minutes, 15 minutes, 20minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50minutes, 55 minutes, 60 minutes, 65 minutes, 70 minutes, 75 minutes, 80minutes, 85 minutes, 90 minutes, 95 minutes, 100 minutes, 105 minutes,110 minutes, 115 minutes, or 120 minutes. Incubation for removal ofembedding material can be conducted for a duration from about 1 minuteto about 20 minutes, from about 1 minute to about 30 minutes, from about1 minute to about 60 minutes, from about 1 minute to about 120 minutes,or from about 5 minutes to about 20 minutes. Incubation for removal ofembedding material can for example be conducted at a temperature of atleast about 37° C. for a duration of at least about 1 minute. Incubationfor removal of embedding material can be conducted in the presence of analkaline buffer or a neutral buffer (e.g. lysis buffer). An alkalinebuffer (e.g. lysis buffer) can have a pH of at least about 8.5, 9.0,9.5, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, or 13.5. A neutral buffercan have a pH of about 7.0 (e.g., from about 7 to about 8).

Tissues or cells can be disrupted or lysed, releasing nucleic acids forseparation, purification, or extraction. Tissue disruption or cell lysiscan be conducted using techniques including but not limited tomechanical stress, sonication, electroporation, osmotic pressure,chemical treatment (e.g., acid or base), enzymatic treatment, heattreatment, and combinations thereof. For example, pressure can be usedto drive tissue through a structure (e.g., a channel, a resin such as afrit or porous resin, or a glass material) to mechanically disrupttissue or lyse cells. In some cases, the trailing electrolyte buffer cancomprise one or more tissue disruption agents and/or cell lysis agents.In some cases, the leading electrolyte buffer can comprise one or moretissue disruption agents and/or cell lysis agents. In some cases,removal of embedding material can be achieved by the same process astissue disruption or cell lysis. For example, incubation at an elevatedtemperature (e.g. from about 30° C. to about 80° C., from about 50° C.to about 80° C., or from about 30° C. to about 65° C.) can achieveremoval of embedding material, tissue disruption, and cell lysis. Tissuedisruption or cell lysis can be conducted off-device or on-device. Inone example, a tissue sample is disrupted in a vessel and subsequentlyloaded onto a fluidic device. In another example, a tissue samplepreviously loaded onto a fluidic device is disrupted on the device.

Samples comprising tissue or cells can be lysed before or after loadingonto a fluidic device using a lysis solution or buffer compatible withisotachophoresis. Lysis buffers compatible with isotachophoresis caninclude non-ionic surfactants or detergents, ionic or zwitter-ionicsurfactants or detergents, chaotropic agents, disulfide bond reducingagents, proteases, nucleases, and other additives or components thatdigest, denature, disrupt, or degrade for the purpose of extracting,purifying, enriching (concentrating), or otherwise isolating nucleicacids. In some cases, a lysis buffer may comprise an alkaline buffer. Insome cases, a lysis buffer may not comprise an alkaline buffer. Anexemplary lysis buffer may include 0.5 M to 9.5 M, 4M to 9 M, or 6.5M to7 M urea as described herein. An exemplary lysis buffer may include 0.5M to 3.5 M or 1.5 M to 2.5 M thiourea as described herein. An exemplarylysis buffer may include 0.5-9.5 M urea and thiourea, for example 7Murea and 2M thiourea with a non-ionic surfactant as described herein.The use of urea alone or in combination with thiourea may be used tolyse cells for nucleic acid purification. In combination, urea andthiourea may act synergistically to lyse cells and may provide anuncharged isotachophoresis-compatible buffer for nucleic acidpurification.

An exemplary lysis buffer may include a non-ionic surfactant such as0.05-0.5% v/v IGEPAL CA-630 as described herein. In some cases, thelysis buffer may comprise one or more trailing electrolytes. In somecases, the lysis buffer may comprise a trailing electrolyte buffer withadditives for tissue disruption or cell lysis as described herein. Insome cases, the lysis buffer may comprise one or more leadingelectrolytes. In some cases, the lysis buffer may comprise a leadingelectrolyte buffer with additives for tissue disruption or cell lysis asdescribed herein. In some cases, the lysis buffer may comprise one ormore leading electrolyes and one or more trailing electrolytes. In somecases, the lysis buffer may comprise one or more leading electrolyes andone or more trailing electrolytes with additives for tissue disruptionor cell lysis as described herein.

In some cases, a method or process herein may involve lysing a cell ortissue sample using a lysis buffer that minimizes mechanical disruptionof DNA and/or RNA during the lysis reaction. For example, cells ortissue may be lysed in a buffer solution containing Tris (e.g., 5 mM, 10mM, 20 mM, 30 mM Tris) with HCl (e.g., 1 mM, 5 mM, 10 mM HCl) and anon-ionic surfactant. The non-ionic detergent (e.g., IGEPAL CA-630) maybe present at about 1%, about 2%, about 3%, about 4%, or greater in thelysis buffer, or less than about 1%. Cells or tissue may be lysed in thelysis buffer by gentle mixing such as by inversion and low-speed(automated pipette). An enzyme such as proteinase K may, in some cases,be included in the lysate or lysis buffer. In some cases, the lysis isconducted without centrifugation. In some cases, centrifugation is usedin the lysis method. The lysate may be introduced into anisotachophoresis device in order to purify a desired analyte such ashigh molecular weight DNA fragments.

Proteins in a sample can be digested, for example via enzymaticdigestion with proteases. Proteases can include but are not limited toProteinase K, proteases, endoproteinases (e.g., trypsin, LysC, GluC,AspN), peptidases, pepsin, and papain. Other protein or polynucleotidedigestion or degradation agents can be used, such as lysozymes.Digestion of proteins can remove crosslinking proteins from crosslinkednucleic acids, converting them into non-crosslinked nucleic acids.Digestion of proteins can occur at room temperature or at elevatedtemperatures described herein (e.g. greater than about 25° C.).

Sample can be processed on a device (e.g., an electrokinetic device orsystem with at least one reservoir connected to at least one channel),such that the sample volume passes through the reservoir into thechannel with less than 20% of the sample volume left behind in thereservoir, and subsequently an ionic current can be applied through thesample volume in the channel. The ionic current may not substantiallypass through the channel. In some cases, less than 50%, 45%, 40%, 35%,30%, 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%,7%, 6%, 5%, 4%, 3%, 2%, or 1% of the sample volume is left behind in thereservoir.

Sample can be processed on a device (e.g., an electrokinetic device orsystem with at least one reservoir connected to at least one channel),such that the sample volume which passes through the reservoir into thechannel is at least 50% of the sample volume loaded into the reservoir,and subsequently an ionic current can be applied through the samplevolume in the channel. In some cases, at least 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 99%, or more of the sample volume is moved fromthe reservoir to the channel. In some instances, the total volume loadedinto the reservoir is less than or equal to an internal volume of thereservoir. The ionic current may not substantially pass through thechannel. In some cases, applying an ionic current comprises conductingisotachophoresis.

Isotachophoresis Devices

Isotachophoresis and/or sample preparation (e.g., deparaffinization,digestion, lysis) can be conducted in a fluidic device, for example amicrofluidic chip. For example, FIG. 5A shows a schematic of a channelwith a sample preparation (e.g., deparaffinization) zone 500 with asample inlet 501 and a trailing electrolyte reservoir 502, apurification (e.g., isotachophoresis) zone 510 with a leadingelectrolyte reservoir 511, and an elution outlet 520. A capillarybarrier may provide an interface between the sample fluid and theleading electrolyte buffer prior to applying voltage. A capillarybarrier may be provided between the sample preparation zone 500 and thetrailing electrolyte reservoir 502 in order to limit, reduce, or preventmixing or pressure-driven flow of the sample fluid and the trailingelectrolyte buffer. A capillary barrier may be provided between thepurification zone 510 and the leading electrolyte reservoir 511 so as tolimit, reduce, or prevent mixing or pressure-driven flow of the contentsof zone 510 and the leading electrolyte reservoir 511. In anotherexample, deparaffinization can be performed first off-chip, or can beunnecessary due to the starting material, in which case the channel cancomprise a lysis and digestion zone (e.g., pH 7, 56° C.) and a crosslinkremoval and purification (e.g., isotachophoresis) zone (e.g., pH 7, 80°C.). In another example, deparaffinization can be performed firstoff-chip, or can be unnecessary due to the starting material, in whichcase the channel can comprise a lysis and digestion zone (e.g., pH 7,temperature T1) and a crosslink removal and/or purification (e.g.,isotachophoresis) zone (e.g., pH 7, temperature T2). In another example,deparaffinization can be performed first off-chip, or can be unnecessarydue to the starting material, in which case the channel can comprise adisruption and/or lysis zone (e.g., pH 7, temperature T1) and adigestion and/or purification (e.g., isotachophoresis) zone (e.g., pH 7,temperature T2). In another example, deparaffinization can be performedfirst of-chip, or can be unnecessary due to the starting material, inwhich case the channel can comprise a disruption and/or lysis zone(e.g., pH 7, temperature T1) and an isothermal enzymatic amplificationzone (e.g., pH 7, temperature T2). In another example, deparaffinizationcan be performed first of-chip, or can be unnecessary due to thestarting material, in which case the channel can comprise a disruptionand/or lysis zone (e.g., pH 7, temperature T1) and an isothermalenzymatic digestion zone (e.g., pH 7, temperature T2). In some cases,the channel may comprises three zones, for example a disruption and/orlysis zone (e.g. pH 7, temperature T1), an isothermal enzymaticamplification zone (e.g., pH 7, temperature T2), and a purification(e.g. isotachophoresis) zone (e.g. pH 7, temperature T3). FIG. 5B showsan exemplary fluidic device cartridge with eight parallel channels eachas shown in FIG. 5A. FIG. 5C shows a top-view schematic of the fluidicdevice shown in FIG. 5B, while FIG. 5D and FIG. 5E show side and endviews, respectively. The devices can comprise sample inlets orreservoirs 530, ITP electrolyte buffer reservoirs 531, and sampleelution outlets or reservoirs 532. The channels and/or reservoirs may becoupled to one or more pneumatic ports. Each of the eight parallelchannels of the fluidic device may be independently operated from eachof the other channels. In some cases, each channel has a dedicated setof electrodes and electric circuitry to drive ITP. Electrodes may forexample be located in the trailing electrolyte reservoir 502 and theleading electrolyte reservoir 511 such that the electrodes do notdirectly contact sample material.

In some instances, there is little or no fluid or ion flow betweenparallel channels. In some cases, the parallel channels may not be influid communication with one another. The fluid leakage rate betweenparallel channels may be less than about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7, 0.8, 0.9, or 1 μL per hour.

In some instances, there is little or no electrical communicationbetween parallel channels such that the parallel channels areelectrically isolated from one another. Each of the parallel channelsmay be independently electrically controlled so as to apply anindependent electric field to each of the channels. In some instances,current leakage between the channels is less than about 0.1 microamperes(μA), 0.2 μA, 0.3 μA, 0.4 μA, 0.5 μA, 0.6 μA, 0.7 μA, 0.8 μA, 0.9 μA, or1 μA. In some instances, the impedance between channels may be greaterthan 0.1 mega Ohm (MOhm), 0.2 MOhm, 0.3 MOhm, 0.4 MOhm, 0.5 MOhm, 0.6MOhm, 0.7 MOhm, 0.8 MOhm, 0.9 MOhm, 1 MOhm, 5 MOhm, 10 MOhm, 20 MOhm, 30MOhm, 40 MOhm, or 50 MOhm.

In some instances, each zone on the isotachofluidic device can beheated. In some instances, the zones are heated to the same temperature.In some instances, individual zones are heated to differenttemperatures. In some instances, a first zone may be heated to atemperature above 37° C., for example within a range of about 60° C. toabout 100° C. In some instances a second zone may be heated to atemperature above 37° C., for example within a range of about 40° C. toabout 60° C.

An isotachophoresis fluidic device can comprise one or more reservoirs,including but not limited to buffer loading reservoirs, sample loadingreservoirs (including reservoirs that accept solid, multiphasic, orother inhomogeneous liquids or solutions such as tissue, whole blood, orunlysed cell suspensions), leading electrolyte reservoirs, trailingelectrolyte reservoirs, reagent reservoirs, elution reservoirs (e.g.,for unloading processed samples), and gas or air reservoirs. In somecases, one physical reservoir can be used for multiple purposes, such asbuffer loading and sample loading. Liquid or air reservoirs can be usedto apply external pressure for liquid loading (e.g., positive pressureon liquid wells or vacuum on gas only reservoirs).

Reservoirs can be in thermal communication with a heating or coolingsource, allowing control of the temperature of the reservoir and anymaterial within (e.g., reagent, sample, product). For example, anelution reservoir can be thermally controlled to control the temperatureof the eluted product (e.g., for preservation of structure, integrity)while within the fluidic device.

Reagent reservoirs can be used to load one or more reagents forprocessing the sample before, during, or after isotachophoresis.Reagents can include digestion reagents, amplification reagents, reversetranscription reagents, linear polymer solutions for size-basedseparations, probes for hybridization reactions, ligation reagents,dyes, tracers, labels, and other reagents. Reagent reservoirs can beconnected to a reaction channel, or a reaction section of anotherchannel, where reactions can occur. Heating or cooling can be applied(e.g., with thermal controllers as discussed herein) to catalyzereactions (such as enzymatic reactions with nucleic acids or proteins),to hybridize or melt nucleic acids, or remove intercalated dyes fromnucleic acids (for example, prior to elution). Heating and cooling canalso be used to control a fixed operating temperature for conducting ITP(e.g., cooling can be applied to reduce effects of Joule heating), or tokeep a reservoir (e.g., an elution reservoir) at a fixed temperature(e.g., cooler than room temperature), such as for stable storage ofpurified nucleic acids. Light can be applied (e.g., with light sourcesas discussed herein) for purposes including optical interrogation,fluorescent excitation, and reaction energy or catalysis.

Gas or air reservoirs, or gas or air outlets, can be connected via gaschannels to liquid channels within a fluidic device to allow purging ofair or other gases from the fluidic device (e.g., during liquid fillingof the fluidic device). Gas or air reservoirs, or pneumatic pressureports, can be connected via gas channels to liquid channels to allow forpumping of fluids onto or within the fluidic device (e.g., for pumpingof fluids from reservoirs into channels).

A device can comprise multiple purification (e.g., isotachophoresis)zones in connection with each other. For example, a secondisotachophoresis zone can split from and run in parallel to a firstisotachophoresis zone, allowing splitting of a sample band at aspecified ratio (e.g., based on a ratio of currents between the twozones) for parallel processing.

A fluidic device can comprise multiple purification zones in parallel(see, e.g., FIG. 5C). For example, a fluidic device can comprise morethan one set of purification zones, each with associated reservoirs,inlets, outlets, channels, and any other components described herein(e.g., sample preparation zones, electrodes, heaters, detectors) inparallel, separate from each other and each capable of independentlyprocessing a sample. A fluidic device can comprise at least 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 48, 96, ormore purification zones in parallel. A fluidic device can comprisemultiple channels in parallel. A fluidic device can comprise at least 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 48,96, or more channels in parallel. Components, such as purification zonesor channels, located in parallel can be side-by-side, located indifferent device layers (e.g., horizontal or vertical layers), or placedin different arrangements. Parallel components can be identical, or canbe designed differently but function equivalently or nearlyequivalently. For example, parallel channels can have differentgeometries to allow a smaller overall fluidic device footprint, butstill function similarly. Alternatively, parallel components can bedesigned to function differently, for example to process different typesof samples in parallel, or to subject samples to different operations.In some cases, parallel components can be designed to subject differentsample types to different operations in parallel. In some cases,parallel components can be designed to subject the same sample types todifferent operations in parallel. In some cases, parallel components canbe designed to subject different sample types to the same operations inparallel. In some cases, parallel components can be designed to subjectthe same sample types to the same operations in parallel. In some cases,parallel components can be designed to simultaneously and/orindependently subject two or more samples to one or more operations inparallel. In some cases, a leakage rate between two or more channels (orbetween two or more purification zones) is less than 0.5 μl per hour,less than 1 μl per hour, less than 5 μl per hour, less than 10 μl perhour. In some embodiments, a current leakage rate between two or morechannels (or between two or more purification zones) is less than 0.5ρA, less than 1 μA, less than 5 μA, or less than 10 ρA. In someembodiments, an impedance between channels or zones is greater than 0.5megaOhm, greater than 1 megaOhm, greater than 5 megaOhm, or greater than10 megaOhm.

As discussed herein, a fluidic device can be designed to processdifferent sample volumes. For example, FIG. 6A, FIG. 6B, FIG. 6C, andFIG. 6D show top, side, bottom, and top three-quarters views,respectively, of a rapid purification ITP fluidic device 600 for samplevolumes greater than or equal to about 200 μL. The device comprises achannel 600 connected to sample input wells 601, ITP buffer wells 602,and sample output (elution) wells 603. The ITP buffer wells 602 caninclude an elution buffering reservoir 605, a leading electrolytereservoir 606, a leading electrolyte buffering reservoir 607, and atrailing electrolyte reservoir 608. Elution reservoir 603 may beconnected to elution buffering reservoir 605 by an elution bufferingchannel 609. A capillary barrier may be provided in the elutionbuffering channel 609 to reduce or prevent mixing or pressure drivenflow between the contents of the elution buffering reservoir 605 and theelution reservoir 603. Leading electrolyte reservoir 606 may beconnected to leading electrolyte buffering reservoir 607 by a leadingelectrolyte buffering channel 610. A capillary barrier may be providedin the leading electrolyte buffering channel 610 to reduce or preventmixing or pressure driven flow between the contents of the leadingelectrolyte buffering reservoir 607 and the leading electrolytereservoir 606. Buffering reservoir 605 may contain elution bufferelectrolytes at a higher ionic strength than those in elution reservoir603, while buffering reservoir 607 may contain leading electrolytes at ahigher ionic strength than those in leading electrolyte reservoir 606.The device may further comprise pneumatic ports 604 along its edgeswhich are configured to couple to a pneumatic device, for example avacuum source on a benchtop instrument. The pneumatic ports 604 may becoupled to the channel 600 and reservoirs by gas channels as describedherein. Application of suction at the pneumatic ports 604 may load thesample, leading electrolyte, and elution buffer into the channel 600. Insome cases, the trailing electrolyte buffer fluid remains in thetrailing electrolyte reservoir 608. Suction may be appliedsimultaneously or sequentially to the pneumatic ports 604 so as to loadthe channel 600 simultaneously or in stages, respectively. The samplemay be loaded into a first zone or sub-channel of channel 600 whichextends from the trailing electrolyte reservoir 608 to a capillarybarrier 611 at a 180° low dispersion turn in the channel 600. Thecapillary barrier 611 may provide an interface between the sample andthe leading electrolyte buffer during loading so as to limit, reduce, orprevent mixing or pressure-driven flow. A capillary barrier may beprovided between the trailing electrolyte reservoir 608 and the firstzone or sub-channel so as to limit, reduce, or prevent mixing orpressure-driven flow between the contents of the trailing electrolytereservoir 608 and the sample. The leading electrolyte may be loaded intothe second zone or sub-channel of the channel 600 which extends fromcapillary barrier 611 to capillary barrier 612. The capillary barrier612 may provide an interface between the leading electrolyte buffer andthe elution buffer. The elution buffer may be loaded into a third zoneor sub-channel of channel 600 which extends from capillary barrier 612to elution reservoir 603. In some embodiments, the ITP buffer wells 602may further comprise a trailing electrolyte buffering reservoir (notshown) containing trailing electrolytes at a higher ionic strength thanthose in the trailing electrolyte reservoir 608. The trailingelectrolyte buffering reservoir may be connected to the trailingelectrolyte reservoir 608 by a trailing electrolyte buffering channel(not shown). The trailing electrolyte buffering channel may comprise acapillary barrier to limit, reduce, or prevent mixing or pressure-drivenflow between the contents of the trailing electrolyte bufferingreservoir and the trailing electrolyte reservoir 608.

Electrodes may for example be located in the trailing electrolytereservoir 608, a trailing electrolyte buffering reservoir (not shown),the leading electrolyte reservoir 606, and/or the leading electrolytebuffering reservoir 607 such that the electrodes do not directly contactsample material. The electrodes may be triggered to alter or control theapplied electric field in response to feedback from a sensor, forexample a voltage, current, conductivity, or temperature sensor asdescribed herein. For example, passage of the nucleic acids within theITP zone from the second zone of channel 600 to the third zone ofchannel 600 may be detected and feedback from the detector may triggerthe applied current to change. The current may for example be increased,decreased, or ended according to the protocol of the instrument. Thecurrent may for example be paused (e.g. dropped temporarily to zero) inorder to enable on-chip quantification of the nucleic acids.Alternatively or in combination, the current may be decreased in orderto slow isotachophoresis within the third zone to allow the nucleicacids which may have dispersed upon transition from the leadingelectrolyte buffer to the elution buffer (or second leading electrolytebuffer) time to concentrate further before reaching the elution well603.

The methods and processes provided herein include methods and processesthat use any of the devices provided herein. Devices provided hereinwith multiple channels for processing multiple samples in parallel maybe used in a variety of contexts. In some cases, a method may includeuse of a device to process multiple samples (e.g., by conductingisotachophoresis on such samples) that share a certain feature (e.g.,solid tissue lysate, cell lysate, solid tissue, fixed tissue). In somecases, the multiple samples may be different samples. For example, themethod may involve performing isotachophoresis on a tissue sample in onezone of the device while simultaneously, but independently, conductingisotachophoresis on a different sample such as a cellular sample orsample comprising cross-linked nucleic acids.

In some cases, a method or multiplexing process provided herein mayinvolve conducting isotachophoresis on a sample in a channel in parallelwith conducting isotachophoresis on a second sample in a second channelusing leading electrolyte and/or trailing electrolyte buffers that arethe same or similar. In some cases, a sample in one of the channels isprocessed using a first leading electrolyte buffer and a sample in adifferent channel is processed using a second leading electrolyte bufferthat is different from the first. For example, the first leadingelectrolyte buffer can contain one or more leading electrolyte ions thatare different from those contained in the second leading electrolytebuffer. In another example, the first leading electrolyte buffer cancontain one or more leading electrolyte ions that are the same as thosecontained in the second leading electrolyte buffer but the concentrationof such leading electrolyte ions in the first leading electrolyte bufferis different from the concentration of such ions in the second leadingelectrolyte buffer. In some cases, a method or process provided hereinmay involve conducting isotachophoresis on a sample in a channel inparallel with conducting isotachophoresis on a second sample in a secondchannel using trailing electrolyte or trailing electrolyte buffers thatare the same or similar. In some cases, a sample in one of the channelsis processed using a first trailing electrolyte buffer and a sample in adifferent channel is processed using a second trailing electrolytebuffer that is different from the first. For example, the first trailingelectrolyte buffer can contain one or more trailing electrolyte ionsthat are different from those contained in the second trailingelectrolyte buffer. In another example, the first trailing electrolytebuffer can contain one or more trailing electrolyte ions that are thesame as those contained in the second trailing electrolyte buffer theconcentration of such trailing electrolyte ions is different in thefirst trailing electrolyte buffer is different from the concentration inthe second trailing electrolyte buffer.

In some embodiments, one or more reservoirs may be connected to twochannels or sub-channels. For example, elution reservoir 603 may beconnected to both channel 600 and elution buffering channel 609.Alternatively or in combination, leading electrolyte reservoir 606 maybe connected to both channel 600 and leading electrolyte bufferingchannel 610. Alternatively or in combination, trailing electrolytereservoir 608 may be connected to both 600 and a trailing electrolytebuffering channel. Alternatively or in combination, sample input well601 may be connected to a mid-point in channel 600 such that channel 600extends to the left (as a first sub-channel) and right (as a secondsub-channel) of the input well 601. The two channels or sub-channels maybe connected to the one or more reservoirs with an angle between the twochannels (swept in the major plane of the fluidic device) of at leastabout 5°, 10°, 20°, 30°, 40°, 45°, 50°, 60°, 70°, 80°, 90°, 100°, 110°,120°, 130°, 135°, 140°, 150°, 160°, 170°, or 180°. The two channels orsub-channels may be connected to the one or more reservoirs with anangle between the two channels (swept in the major plane of the fluidicdevice) of at most about 5°, 10°, 20°, 30°, 40°, 45°, 50°, 60°, 70°,80°, 90°, 100°, 110°, 120°, 130°, 135°, 140°, 150°, 160°, 170°, or 180.

The device may comprise, for example, 8 channels as shown. Each channelmay hold a sample volume of about 50 μL to about 275 μL and a totalvolume of about 500 μL. The 180° low dispersion turn in each channel mayfacilitate such large sample volumes in an 8-channel multi-channel platewith a standard SLAS footprint.

FIG. 7A, FIG. 7B, FIG. 7C, and FIG. 7D show top, side, bottom, andbottom three-quarters views, respectively, of a rapid purification ITPfluidic device 700 for sample volumes less than or equal to about 100μL. The device comprises sample input wells 701, ITP buffer wells 702,and sample output (elution) wells 703. The device 700 may besubstantially similar to device 600 but with different channel geometry(and corresponding reservoir geometry) that does not include a 180° turnin the channel.

The device may comprise, for example, 8 channels as shown. Each channelmay hold a sample volume of about 10 μL to about 100 μL. A device withsmaller sample volumes may be useful for PCR cleanup or other reactioncleanup applications or for smaller sample sizes (for example a samplewith a low number of cells or a small amount of tissue).

FIG. 8A, FIG. 8B, FIG. 8C, and FIG. 8D show top, side, bottom, andthree-quarters bottom views, respectively, of another rapid purificationITP fluidic device 800 for sample volumes less than or equal to about100 μL. The device comprises sample input wells 801, ITP buffer wells802, and sample output (elution) wells 803. The device 800 may besubstantially similar to devices 600 and 700 but comprises multipledifferent channel geometries on a single chip.

The fluidic device can comprise one or more electrodes that apply anelectric field to a fluidic device or a part of the fluidic device.Applied electric fields can be used for conducting isotachophoresis. Thefluidic device may comprise one or more electrodes that apply a singleelectric field to all channels of the fluidic device. The fluidic devicemay comprise one or more electrodes that apply more than one electricfield to the fluidic device, for example one electric field per channelon the device. In some instance, a first and second electric field aregenerated from a single electrode pair. In some instances, a first andsecond electric field are generated from different electrode pairs. Theelectric fields may be applied simultaneously, sequentially, and/orindependently or one another. Electrodes can be external, such as a wirethat drops into a reservoir. Electrodes can be internal, such as amicrofabricated, printed, or other embedded element included within thefabrication of the fluidic device. Electrode materials can include butare not limited to metals (e.g., platinum, titanium), and carbon.

The one or more electrodes of the fluidic device may be part of one ormore electric circuits that apply an electric field to a fluidic deviceor part of a fluidic device. The fluidic device may comprise one or moreelectric circuits that apply a single electric field to all channels orisotachoporesis regions of zones of the fluidic device. The fluidicdevice may comprise one or more electric circuits that apply more thanone electric field to the fluidic device, for example one electric fieldper channel on the device. In some instance, first and second electricfields may be generated from a single electric circuit. In someinstances, first and second electric fields may be generated fromdifferent electric circuits. The electric fields may be appliedsimultaneously, sequentially, and/or independently or one another by theone or more electric circuits. In some instances the device (or benchtopinstrument) may be configured to control a first electric circuitsimultaneously with and independently of a second electric circuit.

Electrodes can be located in reservoirs, such as trailing and leadingelectrolyte reservoirs, which can be separated from sample reservoirs bybuffering channels. In some cases, electrodes are located in bufferingchannels or buffering reservoirs. Location of electrodes in electrolytereservoirs or electrolyte buffering reservoirs can isolate theelectrodes from analytes such as nucleic acids to reduce or eliminatecontamination of electrodes by sample material. This approach can allowreuse of electrodes without cross-contamination between samples. In oneexample, a trailing electrolyte reservoir or trailing electrolytechannel is connected by a buffering channel to a buffering reservoirwhich contains trailing electrolyte ions and an electrode, and thetrailing electrolyte reservoir is also connected to a sample reservoiror sample channel, which in turn is connected to a leading electrolytereservoir by a leading electrolyte channel; the leading electrolytereservoir is also connected by a buffering channel to a bufferingreservoir which also contains leading electrolytes and an electrode. Inanother example, or as a continuation of the previous example, anelution reservoir containing elution buffer is connected to a leadingelectrolyte reservoir by an elution channel and is also connected to abuffering reservoir containing elution buffer electrolytes and anelectrode. The buffering channels between the buffering reservoirs andtheir corresponding reservoirs can include capillary barriers and/or alow cross-sectional area to limit, reduce, or prevent mixing andpressure-driven flow as described herein. The buffering reservoirs maycontain electrolytes at the same or higher ionic strength as theircorresponding reservoirs. For example, the elution reservoir can beconnected to a buffering reservoir containing elution bufferelectrolytes at the same or higher ionic strength or concentration asthe elution reservoir. The trailing electrolyte reservoir can beconnected to a buffering reservoir containing trailing electrolytes atthe same or higher ionic strength or concentration as the trailingelectrolyte reservoir. The leading electrolyte reservoir can beconnected to a buffering reservoir containing leading electrolytes atthe same or higher ionic strength or concentration as the leadingelectrolyte reservoir. Providing dedicated buffering reservoirsconnected to the elution reservoir, trailing electrolyte reservoir,and/or leading electrolyte reservoir with higher ionic strengths canprovide a pool of additional ions to maintain pH and conductivity in thechannel as the sample moves through the channel.

Fluidic devices can be used with one or more thermal controllers. Forexample, FIG. 9A shows a schematic of an eight-plex sample preparationand isotachophoresis device, comprising eight parallel channels 900 ofthe design shown in FIG. SA. FIG. 9B shows a schematic of a first and asecond thermal controller 901, 902. A first thermal controller 901 attemperature T1 (e.g., 80° C.) is aligned with the sample preparationzones of the channels and a second thermal controller 902 at temperatureT2 (e.g., 50° C.) is aligned with the isotachophoresis zones of thechannels. In some cases, additional thermal controllers may be alignedwith additional zones of the channels (not shown), for example a thirdthermal controller at temperature T3 may be aligned with a third zone attemperature T3. In some cases, each zone of each channel can have itsown separate thermal controller, rather than sharing a common thermalcontroller with the respective zones of the other channels. In othercases, all the zones or channels can share one thermal controller. Inother cases, more than one but less than all the zones or channels canshare one thermal controller. Thermal controllers can comprisecomponents including but not limited to resistive heaters, fluid-basedheating or cooling systems, and Peltier devices. Thermal controllers canbe fabricated from materials including but not limited to metals (e.g.,platinum, titanium, copper, gold), carbon, and indium tin oxide (ITO).Thermal controllers can comprise temperature sensors, which can be usedto monitor the temperature being controlled and provide temperaturefeedback for thermal control. Thermal controllers can be used withcomputer control systems, as discussed further in this disclosure. Insome cases, thermal controllers are operated without temperaturefeedback. Thermal controllers can be integrated into fluidic devices orlocated externally, such as within a benchtop system.

Fluidic devices can be used with one or more light sources. Lightsources can be integrated into fluidic devices or located externally toa fluidic device, such as within a benchtop system or in a separatedevice. Light sources can provide light for optical interrogation,fluorescent excitation, temperature sensing, reaction energy orcatalysis, and other purposes.

Fluidic devices can be designed such that their outermost frame ordimensions meet microtiter plate standards (e.g., SLAS microtiter platestandards). Fluidic devices can be designed to use the defined ports ofa microtiter plate (e.g., SLAS standard microtiter plate) as liquidreservoirs, with pneumatic actuation ports located on the unused surfaceexternal to the liquid reservoirs. Pneumatic ports can be arranged atthe edges of a fluidic device with a microtiter plate-compatible layoutsuch that cross-contamination through pneumatic actuation across liquidreservoirs is avoided, and such that the ports are easy to access withpneumatic hardware. A subset of defined ports can also be used forpneumatic actuation in addition to their other functions. In some cases,a fluidic device can be designed and fabricated in two interlockingparts: first, an insert that includes a channel unit (e.g. a layer witha flat surface enabling ease of film bonding), wells, and pneumaticports; and second, an outer ring to provide conformity to a microtiterplate standard (e.g., SLAS microtiter plate dimensional standards),including alignment features for aligning the fluidic device to abenchtop system and mating features to interlock with the first part.Wells can be connected to form bosses, which can be more compatible withinjection molding.

Fluidic devices can be made from a variety of materials, including butnot limited to, glass (e.g., borosilicate glass), silicon, plastic, andelastomer. Plastics can include polymethylmethacrylate (PMMA), cyclicolefin copolymer (COC), cyclic olefin polymer (COP), polyethylene,polyethylene terephthalate (PET), high-density polyethylene (HDPE), andlow-density polyethylene (LDPE). Elastomers can includepolydimethylsiloxane (PDMS).

Materials used for the fabrication of fluidic devices can be selectedfor their optical properties. For example, materials can be used thatexhibit low auto-fluorescence, low scatter, and high transmission atwavelengths of interest (e.g., excitation and emission wavelengths fornucleic acid labels or dyes). Different materials can be used in onefluidic device; for example, a detection region can be fabricated withmaterials exhibiting useful optical properties, while other regions ofthe device can comprise other materials.

Materials used for the fabrication of fluidic devices can be selectedfor their thermal properties. For example, materials can be selected forhigh thermal conductivity. Alternatively, materials can be selected forlow thermal conductivity (e.g., to thermally insulate a fluidic deviceor a region of a fluidic device. Different materials can be used in onefluidic device; for example, a heating region can have materials withhigh thermal conductivity for improved thermal communication with athermal controller, while the heating region is surrounded by materialswith low thermal conductivity for thermal isolation from other regionsof the device.

Materials used for the fabrication of fluidic devices or microchannelstherein can be selected for their elastomeric or deformation properties.For example, materials can be selected for low elasticity so as to allowfor plastic channel closure as described herein. Alternatively,materials can be selected for high elasticity. Different materials canbe used in one fluidic device; for example poly(methyl methacrylate)(PMMA), cyclic olefin copolymer (COC), cyclo-olefin polymer (COP), orthe like can be used in a single fluidic device. Materials may have amodulus of elasticity of at least 1 GPa, 1.5 GPa, 2 GPa, 2.5 GPa, 3 GPa,3.5 GPa, 4 GPa, 4.5 GPa, or 5 GPa. Materials may have a modulus ofelasticity of at most 1 GPa, 1.5 GPa, 2 GPa, 2.5 GPa, 3 GPa, 3.5 GPa, 4GPa, 4.5 GPa, or 5 GPa. Materials may have a tensile strength of atleast 10 MPa, 20 MPa, 30 MPa, 40 MPa, 50 MPa, 60 MPa, 70 MPa, 80 MPa, 90MPa, 100 MPa, 110 MPa, 120 MPa, 130 MPa, 140 MPa, 150 MPa, 160 MPa, 170MPa, 180 MPa, 190 MPa, 200 MPa. Materials may have a tensile strength ofat most 10 MPa, 20 MPa, 30 MPa, 40 MPa, 50 MPa, 60 MPa, 70 MPa, 80 MPa,90 MPa, 100 MPa, 110 MPa, 120 MPa, 130 MPa, 140 MPa, 150 MPa, 160 MPa,170 MPa, 180 MPa, 190 MPa, 200 MPa.

In some cases, surfaces of a fluidic device can be used without surfacetreatments or coatings. In other cases, surfaces of a fluidic device canbe used with surface coatings, such as hydrophobic treatments,hydrophilic treatments, or selective binding agents (e.g., antibodies).Different regions of a fluidic device can comprise different surfacetreatments (or the lack thereof). For example, some channels,reservoirs, or parts thereof can be hydrophobic, while others arehydrophilic.

Fluidic devices can include a range of flow control units andtechniques, including but not limited to capillary barriers, air outletreservoirs, gas/air lines, fill level monitors (e.g., by electrodemeasurement), particular reservoir geometries, particular fluidicresistances of channels, and fluid loading orders.

Capillary barriers can be paired with air outlet reservoirs to purge air(e.g., to prevent bubbles), thereby positioning and successfullyestablishing a liquid-liquid interface (i) between leading and trailingelectrolyte solutions that is required for isotachophoresis, and (ii)between buffering reservoirs and leading electrolyte or trailingelectrolyte and/or sample solutions. Capillary barriers can be designedin combination with channel geometry to automate filling of channels ina preferred order. Channel resistances can be selected, such as bydesign of channel dimensions, to provide differential fluidicresistances. Ordering of liquid loading can allow the correct formationof liquid-liquid interfaces without air bubbles for performingelectrokinetic processes. In one example, a trailing ion reservoir isdirectly connected to the analyte or sample channel.

Gas (e.g., air) channels or lines can be used to provide actuatedpneumatic pressure to capillary barriers or other regions of a fluidicdevice. Gas channels can connect to external gas pressure sources viapneumatic ports. Gas channels can have higher fluidic resistance thanthe liquid channels they provide pressure to, for example to reduce orprevent liquid flow into the gas channel. For example, gas channels canhave less than half the cross sectional area of a main isotachophoresischannel. Multiple gas channels can be connected to a single gasreservoir or port (e.g., with branching channels). Capillary valves canbe employed with branched air lines to prevent upstream liquid movement.FIG. 10A shows an exemplary gas channel 1001 which may comprise acapillary barrier 1002 connected to the liquid channel interface 1003between the sample 1004 and leading electrolyte buffer 1005sub-channels. FIG. 10B is a magnified schematic of the gas channel 1001highlighting the capillary barrier 1002 which prevents upstream liquidmovement towards the pneumatic port 1006.

Negative pressure or vacuum can be applied to the gas channels via thegas ports in order to load a fluidic channel. Each fluidic channel on amicrofluidic device may be loaded simultaneously or independently (e.g.sequentially) of one another. Within a channel, the fluids may be loadedsimultaneously or independently of one another. For example, leadingelectrolyte buffer, high concentration leading electrolyte buffer,trailing electrolyte buffer, high concentration trailing electrolytebuffer, the elution buffer, high concentration elution buffer, or anycombination thereof may be loaded prior to, simultaneously with, orafter loading the sample. For example, negative pressure may be appliedto the gas ports on one side of the chip to load one or more fluids(e.g. trailing electrolyte buffer, elution buffer, etc.). Subsequently,negative pressure may be applied to the gas ports on the other side ofthe chip to load additional fluids (e.g. leading electrolyte buffer).Alternatively, negative pressure may be applied to all of the gas portsconnected to a channel at the same time. The sample may be loaded byapplying negative pressure or vacuum before, during, or after loading ofthe isotachophoresis buffers. The sample may be loaded without applyingnegative pressure or vacuum, for example by wetting or gravity.

Sensors (e.g., electrodes) can be used to detect liquid filling levelsor bubbles (e.g., via current or voltage sensing) and provide feedback.Geometric features (e.g. constrictions, expansions, or turns) can beused in combination with electrodes to monitor impedance of channels andthereby the time progression of isotachophoresis. For example, duringITP the nucleic acids are focused, and voltage can be used to track thefocused band location in the channel from start to finish. In oneexample, monitoring of fluid expansion into a reservoir (such as anelution reservoir) from a connected channel with smaller cross sectionalarea can be used to determine the time the analyte is eluting, therebyallowing for automated elution and end-process control. In anotherexample, a channel constriction can be designed to allow detection ofthe timing (or triggering) of a step in an electrokinetic process, suchas when the focused analyte is entering a channel zone where a reactionis to take place or where an optical detection event is to take place,allowing control of reaction timing or detector triggering.

Reservoir and channel features can be designed to control or preventpressure driven flow. For example, a reservoir (e.g., sample and elutionreservoirs) can have an internal shape designed so that large changes inliquid height produce only small variations in internal volume at theintended head height as shown in FIG. 11. This can provide more precisecontrol of the liquid volume contained in the reservoir. For otherreservoirs, liquid volume can vary without detriment to a separationprocess; such reservoirs can be designed to have large volume changes inresponse to small liquid height changes, and can help stabilize liquidheight throughout the fluidic device. Low fluidic resistances betweenreservoirs can be used to enable fast equilibration times of headpressures and to enable minimal flow of liquids in channels before,during, or after an electrokinetic process.

Reservoirs can be designed to minimize evaporation, for example bycontrolling the surface area within the reservoir to maintain a constantor fixed volume. Reservoirs can be designed to maximize liquid recoveryfrom the reservoirs, for example by using drafted angle wall designs tominimize dead zones. Reservoirs can be designed to prevent the flow ofliquids in connecting channels into the reservoir during unloading,which can help maintain purity or separation of material (e.g., nucleicacids) being unloaded. Reservoirs can be designed for easy loading orunloading via pipetting, for example by having dimensions amenable toadmitting a pipet tip or having volumes within typical pipet operation.For example, the elution reservoir may be configured to admit a pipettip for extraction of nucleic acids. Reservoirs can be designed orspaced to accept multi-channel pipettors (e.g., having a pitch of about9 mm).

Reservoirs (e.g., sample reservoirs) can be located directly above thechannels to be filled, which can minimize liquid lost in connectingchannels between reservoirs and the channels they fill. Reservoirs(e.g., sample reservoirs) can have a conical shaped bottom and acylindrical through-hole; the large inner diameter at the top of such areservoir can allow it to contain a large volume while the liquidmeniscus at the bottom of the reservoir has a smaller inner diameter,reducing the amount of liquid left behind after dispensing. Such adesign can also reduce or prevent wicking of wetting fluids into concavecorners. In some cases, a through-hole from a reservoir (e.g., samplereservoir) into a channel is less than or equal to about 2 millimeters(mm).

FIG. 11 shows a sample reservoir 1100 configured to reduce the amount ofsample left behind (or lost) in the reservoir 1100 after moving thesample to the connected channel 1101. The low-loss sample reservoir 1100may reduce the amount of sample left in the reservoir 1100 after movingthe sample to the connected channel 1101 without adding or pumping inadditional volume (of sample or other fluid) in to the sample reservoir1100 following or during delivery of the sample into the connectedchannel 1101. The low-loss sample reservoir 1100 may comprise an upperor top portion 1102 with an inner hydraulic diameter D₁ configured tocontain a sample volume prior to loading the sample into the channel1101, a lower or bottom portion 1103 with an inner hydraulic diameter orthrough-hole D₂ and height H₁ configured to contain a sample volumeafter loading the sample into the channel 1101, and a tapered or conicalportion 1104 therebetween. In some cases, the upper portion 1102 and/orthe lower portion 1103 are non-symmetrical, in which case the dimensionsD₁ to D₂ may represent the maximum dimension across of the upper and/orlower portions 1102, 1103, respectively.

The sample reservoir 1100 may be configured to produce a head height H₂of sample left behind which equals or nearly equals the head height H₃of the buffers in the other reservoirs 1110 connected to the channel1101 in order to limit, prevent, or reduce pressure-driven flow andmixing in the channel 1101. A standard buffer reservoir 1110 maycomprise an upper portion 1112 with an inner hydraulic diameter D₃ and alower portion 1113 with an inner hydraulic diameter D₄. Unlike in thesample well, D₃ may be substantially similar to D₄ such that a largervolume of fluid is held within the buffer well 1110 compared to thesample well 1100 when the head heights H₂ and H₃ are equal or nearlyequal.

The sample reservoir 1100 may be configured to hold a sample volume(with or without buffer) of at least about 1 nanoliter (nL), 10 nL, 20nL, 50 nL, 100 nL, 200 nL, 500 nL, 1 microliter (4), 10 μL, 20 μL, 30μL, 40 μL, 50 μL, 60 μL, 70 μL, 80 μL, 90 μL, 100 μL, 200 4, 300 μL, 400μL, 500 μL, 600 μL, 700 μL, 800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, or 10 mL. In some cases, thesample reservoir 1100 may be configured to hold a sample volume within arange of from about 1 nL to about 10 nL.

The inner hydraulic diameter D₁ may be larger than the through-holehydraulic diameter D₂. The inner hydraulic diameter D₁ of the upperportion may be at least about 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm,8 mm, 9 mm, 10 mm, 11 mm, 12, mm 13 mm, 14 mm, or 15 mm. The innerhydraulic diameter D₁ of the upper portion may be at most about 1 mm, 2mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12, mm 13mm, 14 mm, or 15 mm. The inner hydraulic diameter D₂ of the lowerportion may be at least about 0.5 mm, 1 mm, 1.5 mm, 2 mm, 2.5 mm, 3 mm,3.5 mm, 4 mm, 4.5 mm, or 5 mm. The inner hydraulic diameter D₂ of thelower portion may be at most about 0.5 mm, 1 mm, 1.5 mm, 2 mm, 2.5 mm, 3mm, 3.5 mm, 4 mm, 4.5 mm, or 5 mm.

The ratio of D₁ to D₂ may determine the amount of sample left in thesample reservoir after the sample is moved into the channel. In somecases the ratio of D₁ to D₂ is at least about 2:1, 5:1, 10:1, 15:1,20:1, 25:1, 30:1, 35:1, 40:1, 45:1, or 50:1. In some cases the ratio orD₁ to D₂ is at most about 2:1, 5:1, 10:1, 15:1, 20:1, 25:1, 30:1, 35:1,40:1, 45:1, or 50:1. A ratio of D₁ to D₂ may be greater than 2:1 inorder to facilitate moving at least 50% of the sample volume from thelow-loss sample reservoir 1100 into the channel 1101.

The cross-sectional area of the upper portion may be at least about 3mm², 5 mm², 10 mm², 15 mm², 20 mm², 25 mm², 30 mm², 35 mm², 40 mm², 45mm², 50 mm², 55 mm², 60 mm, 65 mm², 70 mm², 75 mm². The cross-sectionalarea of the upper portion may be at most about 3 mm², 5 mm², 10 mm², 15mm², 20 mm², 25 mm², 30 mm², 35 mm², 40 mm², 45 mm², 50 mm, 55 mm², 60mm², 65 mm², 70 mm², 75 mm². The cross-sectional area of the lowerportion may be at least about 0.2 mm², 0.3 mm², 0.4 mm², 0.5 mm², 1 mm²,1.5 mm², 2 mm², 2.5 mm², 3 mm², 3.5 mm², 4 mm², 4.5 mm², 5 mm², 6 mm², 7mm², 8 mm², 9 mm², 10 mm², 11 mm, 12 mm². The cross-sectional area ofthe lower portion may be at most about 0.2 mm², 0.3 mm², 0.4 mm², 0.5mm², 1 mm², 1.5 mm², 2 mm², 2.5 mm², 3 mm², 3.5 mm², 4 mm², 4.5 mm², 5mm, 6 mm², 7 mm², 8 mm², 9 mm², 10 mm², 11 mm², 12 mm².

The ratio of the cross-sectional area of the upper portion to thecross-sectional area of the lower portion may determine the amount ofsample left in the sample reservoir after the sample is moved into thechannel. In some cases, the ratio for the upper portion cross-sectionalarea to the lower portion cross-sectional area is at least about 4:1,5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, 100:1, 150:1,200:1, 250:1, 300:1, 350:1, 400:1, 450:1, 500:1, 600:1, 700:1, 800:1,900:1, 1000:1, 1500:1, 2000:1, or 2500:1. In some cases, the ratio forthe upper portion cross-sectional area to the lower portioncross-sectional area is at most about 4:1, 5:1, 10:1, 20:1, 30:1, 40:1,50:1, 60:1, 70:1, 80:1, 90:1, 100:1, 150:1, 200:1, 250:1, 300:1, 350:1,400:1, 450:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1,or 2500:1.

The tapered portion between the upper portion and the lower portion maycomprise an angle so as to facilitate wetting of sample into the lowerportion and movement of the sample from the low-loss sample well to thechannel. In some cases, the tapered portion of the low-loss samplereservoir may comprise a half-angle between the upper portion and thelower portion of less than about 10°, 20°, 30°, 40°, 45°, 50°, 60°, 70°,80°, or 90°. In some cases, the tapered portion of the low-loss samplereservoir may comprise a half-angle between the upper portion and thelower portion of more than about 10°, 20°, 30°, 40°, 45°, 50°, 60°, 70°,80°, or 90°.

In some cases, the height H₁ of the lower portion can be configured soas to produce a head height of sample left behind which equals or nearlyequals the head height of the buffers in the other reservoirs connectedto the channel in order to limit, prevent, or reduce pressure-drivenflow and mixing in the channel. The height H₁ of the lower portion maybe at least about 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm,or 10 mm. The height H₂ of the lower portion may be at most about 1 mm,2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, or 10 mm.

Reservoirs (e.g., elution reservoirs) can have diameters that are largecompared to the diffusion length scale of analytes (e.g., nucleic acids)to reduce the diffusion of analytes out of a reservoir. In some cases,the reservoir diameter length scale can be on the order of millimeters,and the resulting diffusion time of analyte from the reservoir can be onthe order of hours. Connections between channels and reservoirs (e.g.,elution reservoirs) can be designed without sharp corners, therebyreducing the prevalence of high electric field regions at theseconnections and increasing the residence time of analytes within thereservoir. In some cases, the cross section of a reservoir (e.g.,elution reservoir) normal to the electric field can be significantlygreater than the cross section of the channel normal to the electricfield, thereby reducing the electric field strength in the reservoir andincreasing the residence time of analyte within the reservoir.

In some cases, an elution channel and/or an elution reservoir cancomprise a second leading electrolyte buffer, different in type orconcentration from the first leading electrolyte buffer used in the mainchannel. This can allow purified material to be eluted in the secondleading electrolyte buffer (e.g., an elution buffer or output solution).The effective mobility magnitude of the second leading electrolyte ionswithin the second leading electrolyte buffer can be greater than theeffective mobility magnitude of the nucleic acids. The second leadingelectrolyte buffer can have low ionic strength, for example an ionicstrength compatible with downstream assays (e.g., qPCR, next generationsequencing). In some cases, the second leading electrolyte buffer is thesame as the first leading electrolyte buffer but present at a differentconcentration or ionic strength (e.g., an ionic strength lower than thatof the first leading electrolyte buffer). For example, the first leadingelectrolyte buffer may have an electrolyte ion concentration of 70-100mM (e.g. 70-100 mM Tris HCl) while the second leading electrolyte buffermay have an electrolyte ion concentration of less than 70 mM, less than60 mM, or less than 50 mM (e.g., less than 50 mM Tris HCl).

Channels on a fluidic device can be closed. For example, a mechanicalactuator coupled to a mechanical member can be used to apply pressure tocompletely or partially close a channel (e.g., by deformation of thechannel). Elution reservoirs can be closed off from the ITP channel todefine a fixed elution volume. Channel closing can result in reducedflow or completely blocked flow. Channel closing can result in increasedresistance to fluid flow. In some instances, channel closing canincrease fluidic resistance by a factor of at least 2, 3, 4, 5, 10, 20,30, 40, 50, 60, 70, 80, 90, or 100.

FIG. 12A shows an exemplary mechanical member 1200 which can be used toapply pressure to close or at least partially close the channels 1201 ofa fluidic device 1210, the fluidic device 1210 comprising multiplechannels in parallel (for example the device of FIG. 6C comprising eightindependent parallel channels). The mechanical member 1200 can comprisea comb-like structure with teeth 1202 that line up with two locations1204, 1205 in each of the eight channels of the chip as shown in FIG.12B. Mechanical pressure can be applied by the teeth 1202 to permanentlyor plastically close or at least partially close the channels 1201 tolimit, reduce, or prevent liquid flow to or from the elution reservoirs1203 and control the elution volume. At least partially closing thechannels 1201 may increase resistance to fluid flow between the channels1201 and the elution reservoirs 1203. The mechanical member 1200 may becoupled to a mechanical actuator which generates the force applied tothe channel 1201 by the teeth 1202 of the mechanical member 1200. Themechanical member 1200 may comprise a material with a Young's modulus ofelasticity greater than a Young's modulus of elasticity of the channel1201. One or more teeth 1202 of the mechanical member 1200 may beconfigured to heat a channel 1201. One or more teeth 1202 of themechanical member 1200 may be thermally coupled to a heater or heatingelement. The mechanical member 1200 may optionally comprise a heater orheating element. Heat can optionally be applied by the teeth 1202 topermanently or plastically close the channels 1201. One or more teeth1202 may be heated to a temperature greater than the glass transitiontemperature of at least one wall of one or more channels 1201. FIG. 12Cshows how the sixteen teeth 1202 of the mechanical member 1200 line upwith the sixteen locations 1204, 1205 on the chip 1210 (two perchannel). Each tooth 1202 may be configured to deliver mechanicalpressure to the channel 1201 in order to plastically deform at least onewall of the channel 1201. Each channel 1201 is contacted by themechanical member 1200 and plastically deformed at a first closelocation 1204 and a second close location 1205 to isolate the elutionreservoir volume and increase fluid resistance between the channel 1201and the reservoir 1203. In some instances, a tooth 1202 may applymechanical pressure to the channel location 1204 upstream of thereservoir 1203. In some instances, a tooth 1202 may apply mechanicalpressure to a junction where the reservoir 1203 and the channel 1201meet. In some instances, a tooth 1202 may apply mechanical pressure to ajunction 1205 where the reservoir and a buffering channel meet toprevent fluid communication between the reservoir 1203 and a bufferingreservoir.

In some cases, the mechanical member 1200 may comprise one tooth 1202per channel which aligns with the first close location 1204. Forexample, the channel shown in FIG. 5A does not comprise a buffer channelor reservoir connected to the elution reservoir and thus may not need asecond close location 1205 beyond the elution reservoir. In some cases,the mechanical member 1200 is configured to close each of the channels1201 on a chip 1210 at one or more locations. In some cases, themechanical member 1200 is configured to leave one or more channel 1201on the chip 1210 open such that only a fraction of channels 1201 on thechip 1210 are closed.

The mechanical member 1200 may apply a force of at least 0.25 lbs perchannel via teeth 1202. Each tooth 1202 of the mechanical member 1200may apply a force of at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 3, 4, or 5pounds to a channel 1201.

Channels on a fluidic device (e.g., sample preparation zones,isotachophoresis zones) can have a large enough width, height, ordiameter such that contaminants, such as embedding material (e.g.,paraffin), can deposit on the channel walls while still leaving adequateroom for fluid flow within the channel. In some cases, a channel on afluidic device has a width, height, or diameter of less than or equal to20 millimeters (mm), 19 mm, 18 mm, 17 mm, 16 mm, 15 mm, 14 mm, 13 mm, 12mm, 11 mm, 10 mm, 9 mm, 8 mm 7 mm, 6 mm, 5 mm, 4 mm, 3 mm, 2 mm, 1 mm,0.9 mm, 0.8 mm, 0.7 mm, 0.6 mm, 0.5 mm, 0.4 mm, 0.3 mm, 0.2 mm, or 0.1mm. In some cases, a channel on a fluidic device has a width, height, ordiameter of at least 0.1 mm, 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.7mm, 0.8 mm, 0.9 mm, 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, 18 mm, 19mm, or 20 mm. In some cases, a channel on a fluidic device has a widthwithin a range of about 1 mm to about 3.8 mm. In some cases, a channelon a fluidic device has a height within a range of about 0.1 mm to about1.2 mm.

In some cases, a channel on a fluidic device has a length of at leastabout 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, 18 mm, 19 mm, 20 mm, 25mm, 30 mm, 35 mm, 40 mm, 45 mm, 50 mm, 60 mm, 70 mm, 80 mm, 90 mm, 100mm, 110 mm, 120 mm, 130 mm, 140 mm, 150 mm, 160 mm, 170 mm, 180 mm, 190mm, 200 mm, 210 mm, 220 mm, 230 mm, 240 mm, 250 mm, 260 mm, 270 mm, 280mm, 290 mm, 300 mm, 310 mm, 320 mm, 330 mm, 340 mm, 350 mm, 360 mm, 370mm, 380 mm, 390 mm, 400 mm, 410 mm, 420 mm, 430 mm, 440 mm, 450 mm, 460mm, 470 mm, 480 mm, 490 mm, or 500 mm. In some cases, a channel on afluidic device has a length of less than or equal to about 500 mm, 490mm, 480 mm, 470 mm, 460 mm, 450 mm, 440 mm, 430 mm, 420 mm, 410 mm, 400mm, 390 mm, 380 mm, 370 mm, 360 mm, 350 mm, 340 mm, 330 mm, 320 mm, 310mm, 300 mm, 290 mm, 280 mm, 270 mm, 260 mm, 250 mm, 240 mm, 230 mm, 220mm, 210 mm, 200 mm, 190 mm, 180 mm, 170 mm, 160 mm, 150 mm, 140 mm, 130mm, 120 mm, 110 mm, 100 mm, 90 mm, 80 mm, 70 mm, 60 mm, 50 mm, 45 mm, 40mm, 35 mm, 30 mm, 25 mm, 20 mm, 19 mm, 18 mm, 17 mm, 16 mm, 15 mm, 14mm, 13 mm, 12 mm, 11 mm, 10 mm, 9 mm, 8 mm, 7 mm, 6 mm, 5 mm, 4 mm, 3mm, 2 mm, or 1 mm.

Channels on a fluidic device can have a large enough width, height, ordiameter so as to accommodate a large sample volume. In some cases, achannel on a fluidic device has a width greater than its height so as toreduce a temperature rise due to Joule heating in the channel. In somecases, a channel on a fluidic device has a ratio of width to height ofat least 2:1, 5:1, 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1,55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1. In somecases, a channel on a fluidic device has a ratio of width to height ofat most 2:1, 5:1, 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1,55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1. In somecases, a channel on a fluidic device has a cross-sectional area lessthan about 0.1 mm², 0.2 mm², 0.3 mm², 0.4 mm², 0.5 mm², 0.6 mm², 0.7mm², 0.8 mm², 0.9 mm², 1 mm², 1.1 mm², 1.2 mm², 1.3 mm², 1.4 mm², 1.5mm², 1.6 mm², 1.7 mm², 1.8 mm², 1.9 mm², 2 mm², 2.1 mm², 2.2 mm², 2.3mm², 2.4 mm², 2.5 mm², 2.6 mm², 2.7 mm², 2.8 mm², 2.9 mm², 3 mm², 3.1mm², 3.2 mm², 3.3 mm², 3.4 mm², 3.5 mm², 3.6 mm², 3.7 mm², 3.8 mm², 3.9mm², 4 mm², 4.1 mm², 4.2 mm², 4.3 mm², 4.4 mm², 4.5 mm², 4.6 mm², 4.7mm², 4.8 mm², 4.9 mm², 5 mm², 6 mm², 7 mm², 8 mm², 9 mm², 10 mm², 11mm², 12 mm², 13 mm², 14 mm, or 15 mm². In some cases, a channel on afluidic device has a cross-sectional area more than about 0.1 mm², 0.2mm², 0.3 mm², 0.4 mm², 0.5 mm², 0.6 mm², 0.7 mm², 0.8 mm², 0.9 mm², 1mm², 1.1 mm², 1.2 mm², 1.3 mm², 1.4 mm², 1.5 mm², 1.6 mm², 1.7 mm², 1.8mm², 1.9 mm², 2 mm², 2.1 mm², 2.2 mm², 2.3 mm², 2.4 mm², 2.5 mm², 2.6mm², 2.7 mm², 2.8 mm², 2.9 mm², 3 mm², 3.1 mm², 3.2 mm², 3.3 mm², 3.4mm², 3.5 mm², 3.6 mm², 3.7 mm², 3.8 mm², 3.9 mm², 4 mm², 4.1 mm², 4.2mm², 4.3 mm², 4.4 mm², 4.5 mm², 4.6 mm², 4.7 mm², 4.8 mm², 4.9 mm², 5mm², 6 mm², 7 mm², 8 mm², 9 mm², 10 mm², 11 mm², 12 mm², 13 mm², 14 mm²,or 15 mm². In some cases, a channel on a fluidic device has a minimumlength scale for heat dissipation less than about 1 micrometer (μm), 5μm, 10 μm, 20 μm, 30 nm, 40 μm, 50 μm, 100 μm, 150 μm, 200 μm, 250 μm,300 nm, 350 μm, 400 μm, 450 μm, 500 μm, 550 μm, or 600 μm. In somecases, a channel on a fluidic device has a minimum length scale for heatdissipation more than about 1 micrometer (μm), 5 μm, 10 μm, 20 μm, 30μm, 40 μm, 50 μm, 100 μm, 150 μm, 200 μm, 250 μm, 300 μm, 350 μm, 400μm, 450 μm, 500 μm, 550 μm, or 600 μm.

In some cases, a channel on a fluid device has a total volume of atleast about 1 microliter (4), 10 μL, 20 μL, 30 μL, 40 μL, 50 μL, 60 μL,70 μL, 80 μL, 90 μL, 100 μL, 150 μL, 175 μL, 200 μL, 225 μL, 250 μL, 275μL, 300 μL, 350 μL, 400 μL, 450 μL, 500 μL, 600 μL, 700 μL, 800 μL, 900μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL,10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20mL, 25 mL, 30 mL, 35 mL, 40 mL, 50 mL, 55 mL, 60 mL, 65 mL, 70 mL, 75mL, 80 mL, 85 mL, 90 mL, 95 mL, or 100 mL. In some cases, a channel on afluid device has a total volume of at most about 1 microliter (4), 10μL, 20 μL, 30 μL, 40 μL, 50 μL, 60 μL, 70 μL, 80 μL, 90 μL, 100 μL, 1504, 175 μL, 200 μL, 225 μL, 250 μL, 275 μL, 300 μL, 350 μL, 400 μL, 450μL, 500 μL, 600 4, 700 μL, 800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL, 25 mL, 30 mL, 35 mL, 40mL, 50 mL, 55 mL, 60 mL, 65 mL, 70 mL, 75 mL, 80 mL, 85 mL, 90 mL, 95mL, or 100 mL.

In some cases, a fluidic device comprises more than one channel. Thechannels may be spaced within the fluidic device at a given density. Insome cases, the edge to edge distance between channels is at least about0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.7 mm, 0.8 mm, 0.9 mm, 1 mm,1.25 mm, 1.5 mm, 1.75 mm, 2 mm, 2.5 mm, 3 mm, 3.5 mm, 4 mm, 4.5 mm, 5mm, 5.5 mm, 6 mm, 6.5 mm, 7 mm, 7.5 mm, 8 mm, 8.5 mm, 9 mm, 9.5 mm, or10 mm. In some cases, the edge to edge distance between channels is atmost about 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.7 mm, 0.8 mm, 0.9mm, 1 mm, 1.25 mm, 1.5 mm, 1.75 mm, 2 mm, 2.5 mm, 3 mm, 3.5 mm, 4 mm,4.5 mm, 5 mm, 5.5 mm, 6 mm, 6.5 mm, 7 mm, 7.5 mm, 8 mm, 8.5 mm, 9 mm,9.5 mm, or 10 mm. The density of channels may be defined as a ratio ofthe width of the channels to the space (or distance) between channels.In some cases, the ratio of channel width to distance between channelsis at least about 2:1, 2.5:1, 3:1, 3.5:1, 4:1, 4.5:1, 5:1, 5.5:1, 6:1,6.5:1, 7:1, 7.5:1, 8:1, 8.5:1, 9:1, 9.5:1, 10:1, 11:1, 12:1, 13:1, 14:1,15:1, 16:1, 17:1, 18:1, 19:1, or 20:1.

In some cases, the total volume of all channels within a microfluidicdevice (e.g., chip) is 1 microliter (4), 10 μL, 20 μL, 30 μL, 40 μL, 50μL, 60 μL, 70 μL, 80 μL, 90 μL, 100 μL, 150 4, 175 μL, 200 μL, 225 μL,250 μL, 275 μL, 300 μL, 350 μL, 400 μL, 450 μL, 500 μL, 600 4, 700 μL,800 μL, 900 μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL,19 mL, 20 mL, 25 mL, 30 mL, 35 mL, 40 mL, 50 mL, 55 mL, 60 mL, 65 mL, 70mL, 75 mL, 80 mL, 85 mL, 90 mL, 95 mL, or 100 mL. In some cases, thetotal volume of all channels within a microfluidic device (e.g., chip)is at most about 1 microliter (μL), 10 μL, 20 μL, 30 μL, 40 μL, 50 μL,60 μL, 70 μL, 80 μL, 90 μL, 100 μL, 150 μL, 175 μL, 200 μL, 225 μL, 250μL, 275 μL, 300 μL, 350 μL, 400 μL, 450 μL, 500 μL, 600 μL, 700 μL, 800μL, 900 μL, 1 milliliter (mL), 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL,9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19mL, 20 mL, 25 mL, 30 mL, 35 mL, 40 mL, 50 mL, 55 mL, 60 mL, 65 mL, 70mL, 75 mL, 80 mL, 85 mL, 90 mL, 95 mL, or 100 mL.

Inlets and/or outlets of a fluidic device can be arranged and spacedsuch that they are compatible with standard fluid handling formats. Forexample, inlets and/or outlets can be spaced to line up with wells on a5″×3.33″ titer plate. A device can comprise eight inlets and/or outlets,spaced to correspond with a standard eight-tip pipettor and/or the eightwells in a dimension of a standard 24-, 48-, or 96-well plate. A devicecan comprise twelve inlets and/or outlets, spaced to correspond with astandard twelve-tip pipettor and/or with the twelve wells in a dimensionof a standard 96-well plate. A device can comprise sixteen inlets and/oroutlets, spaced to correspond with a standard sixteen-tip pipettorand/or with the sixteen wells in a dimension of a standard 384-wellplate. A device can comprise twenty-four inlets and/or outlets, spacedto correspond with a standard twenty-four-tip pipettor and/or with thetwenty-four wells in a dimension of a standard 384-well plate. This canenable easier fluid handling from such plates onto the device, forexample via robotic pipet systems or other multi-pipets.

Isotachophoresis can be conducted using a benchtop system or basestation. For example, FIG. 13A shows a benchtop system 1300 forconducting sample preparation and isotachophoresis on a fluidic devicecartridge 1301. The fluidic device cartridge can be loaded onto thebenchtop system as shown, and a lid with matching covers and controls1302 can be lowered onto the fluidic device cartridge. The benchtopsystem can also include a control panel 1303 with a user interface(e.g., touch screen) for operation of the system.

The benchtop system can comprise pressure controls that provide pressureto handle fluids (e.g., sample, buffer, reagents, enzyme solutions,electrolyte solutions) on a fluidic device. The benchtop system canreceive pressure feedback signals to regulate or control the fluidhandling. Fluid handling can be used to load fluids onto a fluidicdevice (e.g., reagents, buffers, samples). Fluid handling can be used toprime fluids (e.g., reagent solutions) into dry channels on a fluidicdevice. Pressure can be regulated using, for example, solenoid valves.

The benchtop system can comprise electrodes or electrical contacts.Electrodes can be part of an electric circuit and can insert intoreservoirs or other openings on a fluidic device to allow application ofan electric field within the fluidic device by the completed circuit.Electrical contacts can couple to corresponding contacts on a fluidicdevice, for example a fluidic device with integrated electrodes.

The benchtop system can comprise one or more detectors or sensors, suchas optical detectors, reflectance sensors, infrared (IR) detectors,electrical detectors, thermal sensors, flow sensors, and pressuresensors, including detectors described further in this disclosure.Optical detectors can include but are not limited to three-axis pointdetectors, complementary metal-oxide semiconductor (CMOS) detectors,charge-coupled device (CCD) detectors, photodiode light sensors,photoresistors, photomultiplier tubes, and phototransistors. Electricaldetectors can include electrodes or other detectors capable of detectinga voltage, voltage differential, current, charge, or other electricalproperty. Electrical detectors can be used to detect the passage of aband of extracted or purified nucleic acids, for example by detecting achange in conductivity at the interface between trailing electrolytesand leading electrolytes. Thermal sensors can include infrared (IR)sensors, probe temperature sensors, thermistors, negative temperaturecoefficient (NTC) thermistors, resistance temperature detectors (RTDs),thermocouples, semiconductor-based sensors, or the like.

The one or more detectors or sensors can be simultaneously orindependently operated and controlled. In some instances, a singlechannel may have a dedicated sensor, for example a thermal or voltagesensor, which operates independently of other sensors dedicated to otherchannels on the microfluidic device. Feedback from the independentsensor may be used to independently control one or more electric fieldson the device. For example, a sensor may detect a change in voltage overtime within a well as described herein and feedback from that sensor maybe used to control the current within the channel. A second sensor mayact on a second channel in a similar, but independent, manner. In someinstances, a sensor may detect a change in current over time within awell and feedback from that sensor may be used to control the voltagewithin the cannel.

The benchtop system can comprise one or more thermal controllers thatcontrol a temperature on a fluidic device or a part of a fluidic device.Thermal controllers can comprise components including but not limited toresistive heaters, fluid-based heating or cooling systems, and Peltierdevices. Thermal controllers can be fabricated from materials includingbut not limited to metals (e.g., platinum, titanium, copper, gold),carbon, and indium tin oxide (ITO). Thermal controllers can comprisetemperature sensors, which can be used to monitor the temperature beingcontrolled and provide temperature feedback for thermal control. Thermalcontrollers can be used with computer control systems, as discussedfurther in this disclosure. For example, temperature sensors (e.g.,infrared sensors) can be used to monitor a change in temperature inchannels on a chip. Such temperature changes can be indicative of alocation of an ITP band (e.g., a band of nucleic acid) during an ITPprocess, which temperature difference can be due to a change inconductivity between the leading electrolytes and trailing electrolytes.In some cases, thermal controllers are operated without temperaturefeedback.

Techniques of the present disclosure (including, e.g., the use offluidic devices and/or benchtop systems discussed herein) can providequick processing times. For example, a sample comprising nucleic acidscan be prepared (e.g., removal of embedding material, tissue disruption,cell lysis, nucleic acid de-crosslinking) and have nucleic acidsextracted or purified for subsequent analysis, use, or storage.

Detection and Quantitation

Techniques of the present disclosure can employ one or more detectors.Detectors can be integrated into fluidic devices or located externallyto a fluidic device. Detectors can be used for quantitation of nucleicacid in a sample, for example by fluorescent measurement or ultraviolet(UV) radiation (e.g., for measurement of quantity or purity, such as bymeasurement of A260/A280), or for providing a qualitative measure of thenucleic acids in the sample. Nucleic acids can be detected while locatedon a fluidic device, for example while within a purification zone (e.g.,ITP channel) or reservoir (e.g., elution reservoir). The concentrationof the nucleic acids may be detected (or calculated based on a quantitymeasurement in a known volume such as in the elution well as describedherein). Nucleic acids can be labeled, such as with dyes, and thefluorescence intensity of the nucleic acids can be measured by adetector and used to quantify the nucleic acids present (see, e.g., FIG.14). Nucleic acids can be labeled prior to loading on a fluidic device,while in a fluidic device, or after recovery from a fluidic device.

Use of a detector can enable quantitation of nucleic acids from sampleswith a high sensitivity or a low limit of detection. For example,nucleic acids can be detected (e.g., in-line in an isotachophoresischannel) at limit of detection of less than or equal to about 1000picograms per microliter (pg/μL), 100 pg/μL, 10 pg/μL, 1 pg/μL, 0.9pg/μL, 0.8 pg/μL, 0.7 pg/μL, 0.6 pg/μL, 0.5 pg/μL, 0.4 pg/μL, 0.3 pg/μL,0.2 pg/μL, or 0.1 pg/μL. Nucleic acids can be detected (e.g., in-line inan isotachophoresis channel) at a limit of detection of less than orequal to about 1000 picograms (pg), 100 pg, 10 pg, 1 pg, or 0.1 pg.

Use of a detector can enable identification or qualification of nucleicacids in a sample. For example, techniques such as nucleic acidamplification (including, e.g., PCR, real-time PCR, andreverse-transcription PCR), hybridization (including, e.g., fluorescentin situ hybridization (FISH) and Q-FISH), and sequencing can be used toidentify the presence or absence of, and optionally quantify, aparticular sequence within nucleic acids in a sample.

Detectors can be used in the control of nucleic acid extraction orpurification operations. For example, a detector can detect a band ofnucleic acids concentrated by isotachophoresis. When the concentratednucleic acids reach a certain location within the device, the processcan be ended (e.g., electric fields can be turned off) and extracted orpurified sample can be recovered from the device.

Detectors can include but are not limited optical detectors andelectrical detectors, thermal sensors, and pressure sensors (e.g.,pressure transducers). Optical detectors can include but are not limitedto three-axis point detectors, complementary metal-oxide semiconductor(CMOS) detectors, charge-coupled device (CCD) detectors, photodiodelight sensors, photoresistors, photomultiplier tubes, andphototransistors. Optical detection can be achieved by LED illuminationpaired with photodiode detection. Electrical detectors can includeelectrodes or other detectors capable of detecting a voltage, voltagedifferential, current, charge, or other electrical property. Forexample, electrical detectors can be used to detect the passage of aband of extracted or purified nucleic acids.

End of Run Triggering

When purifying a sample using ITP, it can be important to accuratelystop applying current when the sample ITP zone is in the elutionlocation (e.g., a channel or a reservoir). The present disclosureprovides techniques for assessing the ITP zone position, which can beused to trigger the end of a purification run. These techniques caninclude measurement of driving voltage, measurement of conductivity, andmeasurement of temperature.

FIG. 15 shows a schematic of an ITP channel 1500, with drivingelectrodes placed in the buffered elution electrode (EH) reservoir 1501and the buffered leading electrolyte (LEH) reservoir 1502, and a groundelectrode placed in the buffered trailing electrolyte (TEH) reservoir1503. Conductivity detector (e.g., capacitively-coupled contactlessconductivity detector (C4D)) electrodes 1504 can be placed outside ofthe chip, such as near the elution reservoir 1505, as shown on the leftside of the figure. The channel can also comprise a leading electrolytereservoir 1506 and a sample reservoir or injection point 1507. Gas portsare indicated by small circles on the far left and right edges of thechannel. Gas ports can be used to automatically load or prime fluidsinto the channels from the attached reservoirs, for example using vacuumor applied pressure.

One method for measuring the position of an ITP band is to measure thevoltage or the resistance of the channel, such as between the drivingelectrode and the ground electrode. In systems with more than twoelectrodes, this measurement may be taken between any pair ofelectrodes. This measurement can be made readily, as the voltage drivingelectrophoresis is also the measurement voltage. Throughout thepurification process, the voltage can increase as the trailing ion fillsthe channel. However, the elution reservoir can have a largecross-section, so the contribution to overall resistance can be small.Hence, changes in the buffer conductivity in this region may notstrongly impact the overall channel resistance, and the voltage can stoprising when the ITP zone enters the elution reservoir. This can be usedas a signal to stop applying current and end the run.

To assess this voltage change, the derivative of voltage can becalculated, for example as shown in FIG. 16. The Lanzcos differentiationmethod can be used to suppress high frequency noise. Thresholds can beset for the derivative, and when the derivative passes the threshold, atrigger is performed. In some cases, introducing additional triggers canimprove the robustness of the control. For example, FIG. 16 shows fourtrigger points. In some cases only two of these triggers are used tochange the driving current (e.g., triggers 1 and 4), while the others(e.g., triggers 2 and 3) are used to mark time points in the run, whichcan improve the timing of trigger 4. FIG. 17 shows derivative analysisof the voltages in FIG. 16, with arrows representing the derivativethresholds used to choose the trigger points.

FIG. 16 shows example data from measuring the driving voltage. Eachvertical line represents a trigger point. The two lines represent twoelectrodes, the electrodes in the EH and LEH reservoirs, with respect tothe ground electrode. Points A, B, C, and D show to the time at whichthe ITP zone is in the corresponding location marked in FIG. 15 (A, B,C, and D; labeled 1508, 1509, 1510, and 1511, respectively). In somecases, the conductivity everywhere in the channel can affect the overalldriving voltage, which may make it more difficult to assess what ishappening near the elution reservoir.

A second method for detecting the position of an ITP band is to make alocalized measurement of the conductivity. This can be done using acapacitively coupled contactless conductivity detector (C4D). Thismethod can use high frequency alternating current to pass through thechannel wall and couple to the electrolyte. This localized measurementcan be taken at the elution reservoir itself. This technique can reduceor remove the ambiguity associated with measurements taken over theentire channel. In this technique, the end of run trigger can be chosenas soon as a change is seen in the conductivity at the elution reservoirconductivity detector, for example as shown in FIG. 18.

C4D detection can be performed with electrodes placed below the elutionchannel. Maximizing the electrode area can reduce the necessary drivingfrequency. For example, driving frequencies can be used from about 100kHz to about 10 MHz, with electrode contact pads between about 0.2 mm²and about 50 mm². C4D sensors can be implemented with electricalcomponents including resistors, capacitors, a diode bridge, andhigh-frequency operational amplifiers, with a high frequency signalsource such as from a direct digital synthesizer. FIG. 19 shows anexemplary schematic of a C4D sensor implementation.

A third method for detecting the position of an ITP band is to make alocalized measurement of temperature near the elution reservoir. Thismeasurement can be made with temperature sensors including athermocouple or an infrared temperature sensor. The sensor can be placedunder the channel near the elution reservoir and can monitor thetemperature over time. When the lower-mobility trailing ions displacethe higher-mobility leading ions (e.g. the LE-TE interface of the ITPzone), the electric field in the channel can increase, and thetemperature can rise. During isotachophoresis, lower mobility trailingelectrolyte ions and higher mobility leading electrolyte ions may meetat an isotachophoresis interface. The ITP interface may comprise thesample nucleic acids concentrated between the leading electrolyte ionsand trailing electrolyte ions. A temperature rise can detect thepresence of the ITP interface between the higher-mobility leading ionsand the lower-mobility trailing ions, and thus also indicates thepresence of the nucleic acids therebetween. This temperature rise can be1-10° C.

FIG. 20A and FIG. 20B show exemplary temperature measurement resultsusing a thermal imaging camera. These images show a clear rise intemperature as the trailing ion enters the channel. FIG. 20A shows atemperature map of an ITP channel taken using a thermal imaging camera;the orientation of the channel is the same as in FIG. 15. FIG. 20B showsa plot of temperature over time at the position of Cursor 1 in FIG. 20A.At about 450 seconds, the ITP interface and trailing ion enters theregion, causing an increase in temperature. This temperature rise can bedetected and used as a triggering signal to alter the electric currentapplied to the channel.

The temperature may be measured at a detection location at or near theelution reservoir (e.g. as shown in FIG. 21). In some instances, thedetection location may be located at least about 5 mm from the elutionreservoir. In some instances, the detection location may be located atleast about 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm,11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, 18 mm, 19 mm, 20 mm, 21mm, 22 mm, 23 mm, 24 mm, or 25 mm from the elution reservoir. In someinstances, the detection location may be located at most about 1 mm, 2mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13mm, 14 mm, 15 mm, 16 mm, 17 mm, 18 mm, 19 mm, 20 mm, 21 mm, 22 mm, 23mm, 24 mm, or 25 mm from the elution reservoir. In some instances, thetemperature sensor may be located at least about 1 mm, 2 mm, 3 mm, 4 mm,5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm,16 mm, 17 mm, 18 mm, 19 mm, 20 mm, 21 mm, 22 mm, 23 mm, 24 mm, or 25 mmfrom the elution reservoir. In some instances, the temperature sensormay be located at most about 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, 18 mm,19 mm, 20 mm, 21 mm, 22 mm, 23 mm, 24 mm, or 25 mm from the elutionreservoir.

The temperature sensor may trigger a change in electric current when achange in temperature is sensed. In some instances, the detected changein temperature is within a range of about 0.2° C. to about 5° C. In someinstances, the detected change in temperature is at least about 0.2° C.,0.3° C., 0.4° C., 0.5° C., 1° C., 2° C., 3° C., 4° C., 5° C., 6° C., 7°C., 8° C., 9° C., or 10° C. In some instances, the detected change intemperature is at most about 0.2° C., 0.3° C., 0.4° C., 0.5° C., 1° C.,2° C., 3° C., 4° C., 5° C., 6° C., 7° C., 8° C., 9° C., or 10° C.

In some cases, detection of the ITP zone, for example by voltagemonitoring, conductivity measurements, or temperature sensing, at one ormore trigger points may cause the benchtop controller to alter theelectric current applied to the microfluidic chip. The change may beapplied immediately upon detection or after a pre-determined delay.Detection of the ITP zone may trigger a decrease, increase, or removalof current. For example, detection of the ITP zone at point C 1510 maytrigger a decrease in current in order to increase the residence time ofthe ITP zone in the channel leading to the elution reservoir.Alternatively or in combination, detection of the ITP zone at point D1511 located at or near the elution reservoir may trigger the removal ofelectric current in order to position the ITP zone (and nucleic acids)or a portion thereof within the elution reservoir, well, or region ofthe channel or chip. In some instances, detection of the ITP zone maytrigger a change in electric current after a pre-determined amount oftime. For example, a detection location (for example 1504 or theposition of cursor 1) may be positioned at or near the elution reservoirat a known distance such that the time needed for the ITP zone to travelbetween the detection location and the elution reservoir can becalculated for a given current. The controller may pre-determine atravel time and detection of the ITP zone at the detection location maytrigger a delayed removal of the current after the pre-determined amountof time. In some instances—detecting the ITP zone at a specificdetection location may offer a space-time relationship of the ITP zonewhich may result in more precise triggering than other sensing methods.

In some cases, detection of the ITP zone at a trigger point may causethe electric current applied to the microfluidic chip to changedirections or paths. For example, the electric current may be triggeredto reverse such that the ITP zone reverses direction of travel withinthe channel. In another example, the system may be triggered to stopapplying current between a first pair of electrodes and begin applyingcurrent to a second pair of electrodes to drive the flow of ions along adifferent path. For example, a channel may be “y-shaped” with a firstchannel leading into two side channels which split from the firstchannel at different directions. Current may initially be driven betweenfirst and second electrodes connected to the first channel and a firstside channel, respectively. Without interruption of current, the ITPzone may travel from the first channel to the first side channel.Detection of the ITP zone at a connection between a first channel andtwo side channels may trigger the first and second electrodes to stopdriving current and third and fourth electrodes connected to the firstchannel and a second side channel, respectively, to begin drivingcurrent. The ITP zone will then travel from the first channel to thesecond side channel. In some cases, the first and third electrodes arethe same electrode. In this way, the trigger may cause the current tochange such that the path of the ITP zone changes along the channel.

Further Processing and Use of Purified Samples

Extracted or purified nucleic acids can be used for sequencing,genotyping, analysis of mutations or polymorphisms, analysis of geneexpression levels, disease diagnosis, disease prediction, cytologicalclassification, paternity or genealogical analysis, or indication ofsuggested treatment modalities.

Extracted or purified nucleic acids can be used in amplificationreactions, including but not limited to loop-mediated isothermalamplification (LAMP), strand displacement amplification (SDA),helicase-dependent amplification (HDA), rolling circle amplification(RCA), nicking enzyme amplification reaction (NEAR), PCR, reversetranscription PCR, real-time PCR, quantitative PCR (qPCR), digital PCR,and methylation-specific PCR.

Extracted or purified nucleic acids can be used in sequencing reactions,including Maxam-Gilbert sequencing, chain termination sequencing (e.g.,Sanger sequencing), shotgun sequencing, pyrosequencing, bridge PCR,colony sequencing, polony sequencing, sequencing by synthesis, ionsemiconductor sequencing, nanopore sequencing, nanoball sequencing,sequencing by ligation, sequencing by hybridization, and single moleculereal-time sequencing.

Extracted or purified nucleic acids can be used in protein bindingassays, such as DNA footprinting assays. For example, DNase (e.g., DNaseI) can be used to randomly cut DNA molecules of interest. The techniquesof the present disclosure can be used to separate digested DNA from theDNase enzymes, preventing further digestion. In some cases, DNasedigestion can be performed off of a fluidic device, and then the samplecan be loaded onto a fluidic device for purification. In other cases,DNase digestion can be performed on a fluidic device, and once digestionis performed, the nucleic acids can be purified on the fluidic device.

Samples, such as fixed or embedded samples (e.g., FFPE samples), can beused for longitudinal studies, genome-wide association studies, andother large-scale analysis across populations.

Vertical or Column ITP

Planar ITP device designs, such as discussed herein, can utilizehorizontal space for ITP bands to travel. To process samples at highthroughput, such as in the 96-well plate format, it can be advantageousto fit an entire ITP separation system for a sample in a givenfootprint, such as 9 mm×9 mm footprint. One way of doing this is toincrease the height of the system to accommodate more sample volume.This can provide the option to increase total sample volumes into themilliliter range and still process samples with reasonable run times.

In some cases, it can be important to reduce or prevent gravity-drivenflow and/or buoyant flow through such a system. It can also be importantto assemble the electrolyte zones needed for ITP without mixing theelectrolytes.

A vertical or column ITP system can comprise several ITP stages, whereeach stage comprises a column (e.g., plastic) with gel (e.g., agarose)or similar material at the bottom. The gel can have high electrolyticconductivity. Each stage can be prepared by introducing an electrolyteon top of the gel. The gel can slow or prevent liquid flow. To createthe column, the stages can be stacked with the trailing electrolyte atthe top and the leading electrolyte at the bottom. Current can then bedriven through the system. Purified analyte can be recovered byde-stacking the columns and pipetting out.

FIG. 22A shows an exemplary schematic of a vertical (or column) ITPsetup. The gels in each stage can support the weight of the water (e.g.,aqueous electrolyte solution) above. The cross sectional area of thecolumn can be approximately 9 mm×9 mm. Such a system can process asample with an approximate cross sectional column area of 9 mm×9 mm. Thedesign can be scaled, for example to 96 samples (columns), with overalldevice dimensions conforming to a standard microtiter plate. FIG. 22Bshows an exemplary image of a vertical ITP set up with an DNA ITP band.The stages are: Trailing Electrolyte High (TEH), Sample, LeadingElectrolyte (LE) and Leading Electrolyte High (LEH). The ITP zone ismoving downward through the system. This image does not show the elutionstage (E, shown in FIG. 22A) which is the final destination of theanalyte.

Computer Control Systems

The present disclosure provides computer control systems that areprogrammed to implement methods of the disclosure. FIG. 13B shows acomputer system 1304 that is programmed or otherwise configured tocontrol sample preparation, sample extraction or purification, ordetection. The computer system 1304 can regulate various aspects ofextraction, purification, and detection processes of the presentdisclosure, such as, for example, application of pressure or electricfields, thermal control, detection, quantitation, feedback, andbeginning or ending a process. The computer system 1304 can be anelectronic device of a user or a computer system that is remotelylocated with respect to the electronic device. The electronic device canbe a mobile electronic device.

The computer system 1304 includes a central processing unit (CPU, also“processor” and “computer processor” herein) 1305, which can be a singlecore or multi core processor, or a plurality of processors for parallelprocessing. The computer system 1304 also includes memory or memorylocation 1310 (e.g., random-access memory, read-only memory, flashmemory), electronic storage unit 1315 (e.g., hard disk), communicationinterface 1320 (e.g., network adapter) for communicating with one ormore other systems, and peripheral devices 1325, such as cache, othermemory, data storage and/or electronic display adapters. The memory1310, storage unit 1315, interface 1320 and peripheral devices 1325 arein communication with the CPU 1305 through a communication bus (solidlines), such as a motherboard. The storage unit 1315 can be a datastorage unit (or data repository) for storing data. The computer system1304 can be operatively coupled to a computer network (“network”) 1330with the aid of the communication interface 1320. The network 1330 canbe the Internet, an internet and/or extranet, or an intranet and/orextranet that is in communication with the Internet. The network 1330 insome cases is a telecommunication and/or data network. The network 1330can include one or more computer servers, which can enable distributedcomputing, such as cloud computing. The network 1330, in some cases withthe aid of the computer system 1304, can implement a peer-to-peernetwork, which may enable devices coupled to the computer system 1304 tobehave as a client or a server.

The CPU 1305 can execute a sequence of machine-readable instructions,which can be embodied in a program or software. The instructions may bestored in a memory location, such as the memory 1310. The instructionscan be directed to the CPU 1305, which can subsequently program orotherwise configure the CPU 1305 to implement methods of the presentdisclosure. Examples of operations performed by the CPU 1305 can includefetch, decode, execute, and writeback.

The CPU 1305 can be part of a circuit, such as an integrated circuit.One or more other components of the system 1304 can be included in thecircuit. In some cases, the circuit is an application specificintegrated circuit (ASIC).

The storage unit 1315 can store files, such as drivers, libraries andsaved programs. The storage unit 1315 can store user data, e.g., userpreferences and user programs. The computer system 1304 in some casescan include one or more additional data storage units that are externalto the computer system 1304, such as located on a remote server that isin communication with the computer system 1304 through an intranet orthe Internet.

The computer system 1304 can communicate with one or more remotecomputer systems through the network 1330. For instance, the computersystem 1304 can communicate with a remote computer system of a user.Examples of remote computer systems include personal computers (e.g.,portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® GalaxyTab), telephones, Smart phones (e.g., Apple® iPhone, Android-enableddevice, Blackberry®), or personal digital assistants. The user canaccess the computer system 1304 via the network 1330.

Methods as described herein can be implemented by way of machine (e.g.,computer processor) executable code stored on an electronic storagelocation of the computer system 1304, such as, for example, on thememory 1310 or electronic storage unit 1315. The machine executable ormachine readable code can be provided in the form of software. Duringuse, the code can be executed by the processor 1305. In some cases, thecode can be retrieved from the storage unit 1315 and stored on thememory 1310 for ready access by the processor 1305. In some situations,the electronic storage unit 1315 can be precluded, andmachine-executable instructions are stored on memory 1310.

The code can be pre-compiled and configured for use with a machine havea processor adapted to execute the code, or can be compiled duringruntime. The code can be supplied in a programming language that can beselected to enable the code to execute in a pre-compiled or as-compiledfashion.

Aspects of the systems and methods provided herein, such as the computersystem 1304, can be embodied in programming. Various aspects of thetechnology may be thought of as “products” or “articles of manufacture”typically in the form of machine (or processor) executable code and/orassociated data that is carried on or embodied in a type of machinereadable medium. Machine-executable code can be stored on an electronicstorage unit, such memory (e.g., read-only memory, random-access memory,flash memory) or a hard disk. “Storage” type media can include any orall of the tangible memory of the computers, processors or the like, orassociated modules thereof, such as various semiconductor memories, tapedrives, disk drives and the like, which may provide non-transitorystorage at any time for the software programming. All or portions of thesoftware may at times be communicated through the Internet or variousother telecommunication networks. Such communications, for example, mayenable loading of the software from one computer or processor intoanother, for example, from a management server or host computer into thecomputer platform of an application server. Thus, another type of mediathat may bear the software elements includes optical, electrical andelectromagnetic waves, such as used across physical interfaces betweenlocal devices, through wired and optical landline networks and overvarious air-links. The physical elements that carry such waves, such aswired or wireless links, optical links or the like, also may beconsidered as media bearing the software. As used herein, unlessrestricted to non-transitory, tangible “storage” media, terms such ascomputer or machine “readable medium” refer to any medium thatparticipates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, a tangible storagemedium, a carrier wave medium or physical transmission medium.Non-volatile storage media include, for example, optical or magneticdisks, such as any of the storage devices in any computer(s) or thelike, such as may be used to implement the databases, etc. shown in thedrawings. Volatile storage media include dynamic memory, such as mainmemory of such a computer platform. Tangible transmission media includecoaxial cables; copper wire and fiber optics, including the wires thatcomprise a bus within a computer system. Carrier-wave transmission mediamay take the form of electric or electromagnetic signals, or acoustic orlight waves such as those generated during radio frequency (RF) andinfrared (IR) data communications. Common forms of computer-readablemedia therefore include for example: a floppy disk, a flexible disk,hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD orDVD-ROM, any other optical medium, punch cards paper tape, any otherphysical storage medium with patterns of holes, a RAM, a ROM, a PROM andEPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wavetransporting data or instructions, cables or links transporting such acarrier wave, or any other medium from which a computer may readprogramming code and/or data. Many of these forms of computer readablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processor for execution.

The computer system 1304 can include or be in communication with anelectronic display 535 that comprises a user interface (UI) 1340 forproviding, for example, operational parameters (e.g., processing time,temperature, field strength), nucleic acid quantitation information, orother information. Examples of UI's include, without limitation, agraphical user interface (GUI) and web-based user interface.

Methods and systems of the present disclosure can be implemented by wayof one or more algorithms. An algorithm can be implemented by way ofsoftware upon execution by the central processing unit 1305. Thealgorithm can, for example, regulate thermal controllers, calculatenucleic acid quantitation, control process functions, and begin or end aprocess.

Kits

This disclosure provides kits useful for conducting isotachophoresisprocesses. Generally, such kits comprise a microfluidic device providedherein and one or more buffers. The buffers may include one or moresample buffers, one or more leading electrolyte buffers, one or moretrailing electrolyte buffers, one or more lysis buffers and/or one ormore elution buffers, in any combination. In some cases, the kit may ininclude one or more enzymes (e.g., RNase, DNAs, nucleases, proteases,proteinases, polymerase). The buffers may be supplied in separate tubes.In some cases, the microfluidic device is pre-loaded with one or morebuffers. The kits may include a set of instructions for operating thedevice and/or processing a sample.

EXAMPLES Example 1—DNA Extraction from FFPE Samples

An FFPE sample from a human patient is obtained. A 1.1× aqueous alkalinebuffer solution (Solution A1) is prepared with 80 mM NaOH, 11 mM DTT,and 0.5% v/v Igepal CA-630 in nuclease-free distilled or deionizedwater. A 10× quenching solution (Solution A2) is prepared with 776 mMHCl and 100 mM Tris base or Trizma base in nuclease-free distilled ordeionized water. Commercially available Proteinase K solutions andRNases are also provided. Alternatively, a neutrally-buffered (e.g., pHfrom about 7.0 to about 8.0) 5-50 mM Tris-HCl solution with 0-80 mMNaCl, 5-10 mM DTT, and 0.1-0.5% v/v IGEPAL CA-630 can be prepared innuclease-free distilled or deionized water.

An FFPE section or scroll is added to a 1.5-2.0 mL microcentrifuge tube.175 μL of Solution A1 is added to the tube. The tube contents areincubated for 1-20 minutes at 50-99.9° C. (in some cases, the tubecontents are incubated for 5-20 minutes at 95-99.9° C.) to deparaffinizethe sample. 20 μL of Solution A2 are added to the tube to quenchSolution A1 and achieve a buffered solution with pH of about 7-8.25.Alternatively, an FFPE section or scroll can be incubated in 195 μL ofquenched or neutral buffer (e.g., pH from about 7.0 to about 8.0) for1-30 minutes at 50-80° C. to deparaffinize the sample. Otherdeparaffinization protocols that can be used include (1) treating thesample with xylene, followed by one or more washes with 96%-100% ethanolat room temperature, followed by drying of the tissue; (2) incubatingthe sample at an elevated temperature (e.g., 50-100° C.) for 1-30minutes in a buffered aqueous solution at about pH 7 to about pH 8.25;(3) incubating the sample at an elevated temperature (e.g., 50-100° C.)for 1-30 minutes in an alkaline aqueous solution followed by quenchingto a buffered solution with pH of about 7 to about 8.25; or (4)incubating the sample at an elevated temperature (e.g., 50-100° C.) for1-30 minutes in mineral oil.

5 μL of Proteinase K solution is added to the deparaffinized samplesolution to a final concentration of 400-1000 μg/mL (typically 600-700μg/mL) and a final volume of 200 μL. The solution is then incubated for15-60 minutes at about 56° C. Optionally, the solution is furtherincubated for 2-60 minutes at 80-90° C. Optionally, 3 μL of RNase A (orabout 50-200 μg/mL RNase A) is added to the solution. The solution isthen cooled to room temperature, and the FFPE lysate is loaded onto afluidic device for further processing, such as by isotachophoresis(ITP).

Example 2—Comparison of DNA Extraction Yields

DNA was extracted using a bench top controller device to automateisotachophoresis in a fluidic device from (i) qPCR buffer as a post-PCRclean-up (FIG. 3, triangle data points), and (ii) cell culture lysate(FIG. 3, square data points), with yield calculated using qPCR.Published DNA yield data using a traditional solid-phase extractioncolumn (SPE; FIG. 3, diamond data points) are provided for comparison.FIG. 3 shows DNA yield versus input DNA mass. The leading electrolytebuffer used for isotachophoresis comprised 88 mM Tris with 44 mM HCl.Trailing electrolyte was loaded into the trailing electrolyte reservoirand comprised 1.2M Tris with 0.3 M Caproic Acid and 0.6 M MOPS. Thecellular lysate sample was prepared in a second leading electrolytebuffer (sample buffer) comprising 10 mM Tris with 5.6 mM HCl. Extractionof DNA from human Jurkat cell culture lysate was performed at yieldsfrom about 60% to about 90% for input DNA masses from about 10⁻²nanograms (ng) to about 10³ ng. Cells were lysed in an aqueous solutioncomprising 40 mM NaOH for 1 minute and subsequently quenched at a 1:1volume ratio with a buffered acidic solution to bring the final celllysate sample to 10 mM Tris with 5.6 mM HCl and 20 mM NaCl at pH 8.Proteinase K was added to a final concentration of 400 μg/ml within thecell lysate sample volume and incubated for 10 minutes and 56° C. Thelysed sample was then brought to room temperature and loaded onto thefluidic device for isotachophoresis. Extraction of genomic DNA(pre-purified from human Jurkat cells using a commercial SPE kit) spikedinto a buffer comprising 10 mM Tris-HCl pH 8 was performed at yieldsfrom about 90% to about 100% for input DNA masses from about 10¹ ng toabout 10³ ng.

Compared to traditional SPE column kits, the isotachophoresis method anddevice used here allowed for higher yields. This may have been due to ahigher off-chip lysis efficiency with the indicated lysis chemistryfollowed by a more efficient recovery of nucleic acids usingisotachophoresis. The isotachophoresis methods and devices describedherein may provide lower adsorption of nucleic acids samples to thesurfaces of the chip compared to a standard column and/or lower deadvolumes within the fluidic device than a column. The isotachophoresismethods and devices described herein may enable less biased or unbiasedrecovery of nucleic acids based on length and/or sequence, which mayalso provide for higher efficiency recovery. The spiked-in genomic DNAsample performed had a very high recovery (yield) which may indicatethat isotachophoresis has very little systematic loss of sample due tothe isotachophoresis process itself (whereas the cell lysate sample mayhave other factors which contribute to loss of efficiency such as thelysis chemistries used which may be improved for higher yields).

Example 3—Separation of Crosslinked and Non-Crosslinked Nucleic Acids

A deparaffinized and lysed mouse FFPE tissue sample (processed asdescribed in Example 1) comprising crosslinked and non-crosslinkednucleic acids was loaded onto a fluidic device for isotachophoresis withleading electrolyte and trailing electrolyte. The sample was lysed asdescribed in Example 1 and prepared in a leading electrolyte solution toa final concentration of 10 mM Tris with 5.6 mM HCl. The leadingelectrolyte comprised 140 mM Tris with 70 mM HCl. The trailingelectrolyte comprised a mixture of 2.1 M Tris with 0.5 M caproic acid asa spacer ion with a higher effective mobility magnitude than HEPES and0.7 M HEPES as an ion with a lower effective mobility magnitude. Duringisotachophoresis, non-crosslinked nucleic acids, having a highereffective mobility magnitude, focus ahead of the caproic acid zone andbehind the leading electrolyte zone. Crosslinked nucleic acids andsample contaminants focus behind the caproic acid zone, and either aheadof or within the HEPES zone depending on the degree of crosslinking andtheir effective mobility magnitude. FIG. 23 shows two images of DNAseparation in an isotachophoresis channel subsequent to a two hour(upper) or an overnight (lower) digestion to remove crosslinkingproteins from the DNA. Proteinase K was added to the deparaffinizedlysed tissue (quenched to pH 8.2) at final concentration of 700 μg/mlfor digestion. Crosslinked DNA appears at the left end of the channel,separated by spacer ions from the amplifiable non-crosslinked DNA at theright end of the channel. The graph in FIG. 23 shows intensity of DNAsignal versus position in the channel for the two hour 2301 andovernight 2302 digestions.

Example 4—Extraction and Purification of DNA from Lung and Liver FFPESamples

Formalin-fixed paraffin-embedded (FFPE) mouse lung and liver sampleswere obtained (e.g., Zyagen). Seven pairs of FFPE sections (1 cm by 1 cmby 5-10 μm) were processed, with one section from each pair processed byon-device isotachophoresis and one section processed by a differentmethod (Promega ReliaPrep FFPE DNA kit) for comparison. The leadingelectrolyte buffer used for isotachophoresis comprised 88 mM Tris with44 mM HCl. Trailing electrolyte was loaded into the trailing electrolytereservoir and comprised 1.2M Tris with 0.3 M Caproic Acid and 0.6 MMOPS. Samples were deparaffinized by incubation in a 10 mM Tris-HClbuffer with 10 mM DTT, 72 mM NaCl and 0.5% IGEPAL CA-630 at pH 8.0 forapproximately 1 minute at 80° C., and subsequently treated withproteinase K in the same solution for 60 minutes at 56° C. The digestedsample was then incubated for 15 minutes at 90° C. ITP was conducted onone sample from each pair of sections by dispensing 200 μL ofpre-processed sample mixture, including embedding and FFPE tissuedebris, into the sample inlet of a fluidic device. The other sectionfrom each pair was extracted using Promega's ReliaPrep FFPE gDNA kitaccording to manufacturer's protocol. FIG. 24A shows an image of twoneighboring ITP channels on a fluidic device with DNA from FFPE samples,labeled with intercalating dye for visualization. Extracted DNA from thesamples was quantified with qPCR. FIG. 24B shows the quantifiedextracted DNA in nanograms (ng) for each of the seven sample pairs. Foreach pair, the darker left-hand bar shows results for ITP and thelighter right-hand bar shows results for the ReliaPrep kit. The leftmosttwo sample pairs are human liver samples, and the remaining five samplepairs are human lung samples. For all seven sample pairs, the amount ofamplifiable nucleic acids extracted via ITP is significantly higher(typically about 1.5 to 8 times higher amplifiable yields) than theamount of nucleic acids extracted by the ReliaPrep kit.

Example 5—ITP-Based Quantitation of Nucleic Acids

Quantitation of nucleic acids using ITP was tested and compared to qPCR.The comparison was performed over the full range of sample amounts usingan RNaseP human reference gene assay (ABI). Standard or calibrationcurves were generated from 50 qPCR runs (10 replicates each at 5 ordersof magnitude concentrations) and were used to quantify qPCR measurementuncertainty for this range of DNA amounts.

DNA was extracted from 4 million Jurkat cells using a standard kit(e.g., Invitrogen PureLink Genomic DNA kit). For on-device ITP, Jurkatcells were lysed off-chip using a pH 12.7 NaOH solution for 2 minutes,quenched to buffered solution at pH 7.5-8 using a solution ofhydrochloric acid and Tris base, and then treated with Proteinase K forat pH 8 and 56° C. for 10 minutes.

Pre-purified DNA was processed via ITP and quantified in the ITP channelvia fluorescent intensity. The leading electrolyte buffer used forisotachophoresis comprised 88 mM Tris with 44 mM HCl. Trailingelectrolyte was loaded into the trailing electrolyte reservoir andcomprised 1.2M Tris with 0.3 M Caproic Acid and 0.6 M MOPS. The samplewas prepared in a leading electrolyte buffer (sample buffer) comprising10 mM Tris with 5.6 mM HCl. FIG. 14 shows a titration curve of measuredfluorescent intensity from DNA compared to known DNA sample mass, and islinear over seven orders of magnitude, from 0.4 picograms (pg) to about10⁶ pg. The upper left inset of FIG. 14 shows an image of 250 ng of DNAin an ITP channel. The lower right inset of FIG. 14 shows point detectorfluorescent signal intensity on a logarithmic scale for ITP-extractedDNA in an ITP channel, at 250 pg, 2.5 ng, 25 ng, and 250 ng of DNA.

Example 6—Lack of Bias in ITP Extraction and Purification

Mixtures of synthetic 100 base labeled DNA oligonucleotides with 63% A-Tcontent (37% G-C content, HEX label) and DNA oligonucleotides with 68%G-C content (FAM label) were prepared at three concentrations (1 ng/μL,square data points; 10 ng/μL, diamond data points; 100 ng/μL, triangledata points) and five concentration ratios (overall GC- to AT-rich ratiofrom 0.1 to 10). Ratios were calculated from fluorescence plate readermeasurements obtained pre- and post-processing. FIG. 4A shows acomparison of the output GC- to AT-rich ratio versus the input GC- toAT-rich ratio for ITP processing, demonstrating a lack of bias in theITP process.

A mixture of oligonucleotides from a 1 kb DNA ladder (New EnglandBiosciences) was measured for length before and after processing, usingintegrated signals of electropherogram peaks from the Experion 12k DNAanalysis kit (BioRad). Size distribution within the sample before andafter processing was compared for on-device ITP (FIG. 4B, top), QiagenQiaAmp column kit (FIG. 4B, middle), and Invitrogen PureLink column kit(FIG. 4B, bottom). The leading electrolyte buffer used forisotachophoresis comprised 88 mM Tris with 44 mM HCl. Trailingelectrolyte was loaded into the trailing electrolyte reservoir andcomprised 1.2M Tris with 0.3 M Caproic Acid and 0.6 M MOPS. The samplewas prepared in a leading electrolyte buffer (sample buffer) comprising10 mM Tris with 5.6 mM HCl. For each comparison, the top row shows thesize distribution in the recovered output fraction and the bottom rowshows the initial size distribution in the sample.

Example 7—Off- or On-Chip Proteinase K Digestion of Cell Lysate NucleicAcids

FIG. 25A shows an image of a single channel ITP chip loaded with nucleicacid (RNA extraction and proteolytic digest from human cells) stainedwith dye for visualization. On the left 2501 is an ITP band from sampleprocessed off-chip prior to loading with 200 μg/mL proteinase K insample buffer, while on the right 2502 is a sample not processed withproteinase K. The leading electrolyte buffer used for isotachophoresiscomprised 100 mM Tris with 50 mM HCl. Trailing electrolyte was loadedinto the trailing electrolyte reservoir and comprised 1.8M Tris with 1 MCaproic Acid and 1 M MOPS. The sample was prepared in a leadingelectrolyte buffer (sample buffer) comprising 10 mM Tris with 5.6 mMHCl. FIG. 25B shows an image of a single channel ITP chip loaded withnucleic acid (RNA extraction and proteolytic digest from human cells)stained with dye for visualization. On the left 2501 is an ITP band fromsample processed on-chip 200 μg/mL proteinase K in leading electrolyte,while on the right 2502 is a sample not processed with proteinase K. Inboth cases, the sample processed with proteinase K exhibits a tighterITP band, representing nucleic acids not associated with protein (highereffective mobility magnitude), while the sample not processed withproteinase K exhibits a smeared band, representing nucleic acidassociated with variable amounts of protein (lower effective mobilitymagnitude).

Example 8—RNA Extraction from Human Cells Using Off-Chip Lysis andOn-Chip ITP Purification

FIG. 26A shows an image of an RNA ITP band 2601 in a chip channel duringextraction and purification of RNA from cell lysate (Jurkat cells) withDNA digested. FIG. 26B shows an image of a total nucleic acid ITP band2602 in a chip channel during extraction and purification of RNA fromcell lysate (Jurkat cells) without DNA digested. The leading electrolytebuffer used for isotachophoresis comprised 100 mM Tris with 50 mM HCl.Trailing electrolyte was loaded into the trailing electrolyte reservoirand comprised 1.8M Tris with 1 M Caproic Acid and 1 M MOPS. The samplewas prepared in a leading electrolyte buffer (sample buffer) comprising10 mM Tris with 5.6 mM HCl. FIG. 26C and FIG. 26D show graphs of RNAquality electropherograms (measured using the BioRad Experion) for thesamples shown in FIG. 26A and FIG. 26B, respectively. Cell lysis andDNase digestion were performed in a buffered solution at pH 8 containing7M urea, 2M thiourea, and a non-ionic surfactant as discussed herein.These results demonstrate the preparation of high quality RNA with orwithout DNA digestion.

Example 9—Extraction of Whole Lysed Blood Using ITP and 200 μl ChipDevice

FIG. 27A shows results of DNA yield (ng) for ITP (square) compared tocolumn (diamond, Qiagen QiaAmp) extraction of whole mouse blood as afunction of percent by volume of whole blood in starting sample. FIG.27B shows an image of total nucleic acid in an ITP band 2401 during ITPpurification of lysed whole mouse blood on a chip. The leadingelectrolyte buffer used for isotachophoresis comprised 260 mM Tris with130 mM HCl. Trailing electrolyte was loaded into the trailingelectrolyte reservoir and comprised 2.1 M Tris with 0.5 M Caproic Acidand 0.7 M MOPS. The sample was prepared in a leading electrolyte buffer(sample buffer) comprising 10 mM Tris with 5.6 mM HCl.

FIG. 27C and FIG. 27D show white light and fluorescence overlay imagesof ITP chip channels showing physical separation of heme from the bloodsample in the sample channel and leading electrolyte (or separation)channel 2703 from the elution channel and reservoir 2704, before andafter ITP purification of 50% by volume whole blood lysate 2702. Thepurified nucleic acid is stained with green dye for visualization inelution well. FIG. 27C shows the chip before ITP (blood lysate and ITPbuffers loaded in chip; pure buffer and no DNA in elution well). FIG.27D shows the chip after ITP (blood lysate and ITP buffers loaded inchip; pure buffer and DNA in elution well). FIG. 27E shows the chip postITP purification, with a white light image of the chip channel showingphysical separation of heme from the blood sample in the sample well2705 and leading electrolyte (or separation) channel from the elutionchannel and reservoir 2706 in single channel chip device (50% by volumeblood). FIG. 27F shows the chip post ITP purification, with a whitelight image of the chip channel showing physical separation of heme fromthe blood sample in the sample well 2705 and leading electrolyte (orseparation) channel from the elution channel and reservoir 2706 insingle channel chip device (25% by volume blood).

Example 10—Extraction of High Molecular Weight DNA from Cultured HumanCancer Cells Using Off-Chip Lysis and On-Chip ITP Purification

FIG. 28 shows results of high molecular weight DNA purification for ITP(solid line) compared to solid phase extraction (SPE; dashed line,Qiagen MagAttract) of cultured human Jurkat cells as the percentage ofDNA mass in the purified sample having fragments shorter than a givenlength (Kb). Cell lysis was performed off-chip in a buffered lysissolution containing 10 mM Tris with 5.6 mM HCl and 0.2% v/v IGEPALCA-630. The buffered solution was configured to lyse the cells andreduce mechanical disruption of the DNA during lysis. Cell pellets werelysed in the lysis solution and mixed gently with inversion andslow-speed (automated pipettor), wide-bore tip pipetting (e.g. Rainin200 μl wide bore tip) to aid in homogenization of the lysate. A finalconcentration of 500 μg/ml Proteinase K was added to the lysate andincubated for 20 min at 60° C. ITP was performed on the lysate with 88mM Tris with 44 mM HCl as the leading electrolyte and 1.2 M Tris with0.3 M caproic acid and 0.6 M MOPS as the trailing electrolyte. ITP-basedpurification led to 2 to 3 times greater mean DNA fragment lengths ascompared to the bead-based PSE kit, in part due to reduced mechanicalshearing of the DNA during isotachophoresis compared to SPE due to thelack of a solid phase component or high shear forces (e.g. fromcentrifugation) during the extraction process. The ITP purified DNA hadan average DNA length of about 175 Kb (i.e. 50% of the DNA masscontained DNA fragments greater than about 175 Kb) compared to SPEpurification which yielded DNA with an average length of about 75 Kb.More than 60% of the mass of the DNA extracted by ITP contained anaverage fragment length greater than 150 kB. ITP produced at least aboutthree times as many DNA fragments with a size of at least 150 kB thanthe SPE method.

Example 11—Closing of Channels Using Mechanical Member

FIG. 29A shows a fluidic device comprising 8 closed channels. Eachchannel was permanently closed at two locations 2902, 2902 as shown inFIG. 12B by applying a temperature of 150° C. and a pressure of 30pounds (across all 16 locations; i.e. 1.875 pounds per tooth) to thedevice for 1 second with the comb-like mechanical member of FIG. 12A.FIG. 29B shows a zoomed in microscopic view the second channel closurelocation 2902 adjacent the elution reservoir 2903 of each of thechannels. FIG. 29C shows the percent closure calculated as a function offorce applied to the chips. The extent of channel closure was assessedwithout fluid loaded into the channel. Closure was measured by applyinga constant pressure and measuring air flow rate through the channel.Five chips were assessed. Diamonds indicate closure data obtained fromthe first close location 2901 and triangles indicate closure dataobtained from the second close location 2902. Without a force applied,the channels were open or mostly open. A force of 10 pounds across thedevice was sufficient close most of the channels while a force of 30pounds across the device closed all or nearly all of the channelsrepeatedly. FIG. 29D shows the results of conductivity measurements witha conductivity meter to determine if channels are closed. The chipreservoirs and channels were loaded with ITP buffers as described inFIGS. 12A-12D or FIG. 15 (leading electrolyte, a high concentration ofleading electrolyte for buffering, trailing electrolyte, elution buffer,a high concentration of elution buffer for buffering, and sample bufferwithout a biological sample). The channels were closed using themechanical member and then the fluid in the elution reservoir 2903 waspipetted out of the reservoir and collected. The conductivity of theelution fluid was measured and compared to measurement of theconductivity of original (pre-loaded) elution buffer (same bufferinitially loaded in the chip). It was expected that the conductivity ofmeasured fluid would be the same as the original elution buffer ifchannel closure was sufficient to provide fluidic resistance at thefirst channel close location 2901 between the elution reservoir 2903 andthe channel and at the second channel close location 2902 within thechannel connecting the elution reservoir 2903 to the elution bufferingreservoir (via the elution buffering channel; not shown). For a fullyclosed channel, the conductivity of the eluted volume (withoutperforming ITP) can be equal to the conductivity of the elution bufferalone, indicating no transfer of fluids or ions during collection. Foursituations were tested—without a closer (fully open channels), with thefirst close location 2901 closed (partially closed), with both locations2901, 2902 closed (fully closed), or with every reservoir but theelution reservoir sealed with a film (“Magic Helmet”). In the MagicHelmet situation, the channels were not physically deformed by themechanical member but were instead sealed with a film applied by theoperator in order to increase resistance to fluid flow. Elution volumesfrom partially closed channels showed increased conductivity compared tofully closed channels. Sealing of the non-elution reservoirs with theMagic Helmet were increased compared to fully closed channels as wellbut remained generally less than the conductivity of a 2× elutionbuffer. These conductivity levels were, however, much lower than thoseobtained from eluates without channel closure.

Example 12—Voltage Measurement and End-of-Run Triggering

FIG. 30 shows an exemplary example using measurement of the drivingvoltage to trigger a reduction or removal of an electric current in oneof the channels. A fluidic device comprising 8 channels was loaded withITP buffers (leading electrolyte buffer comprising 88 mM Tris with 44 mMHCl, a high concentration of leading electrolyte for buffering, trailingelectrolyte buffer comprising 1.2 M Tris with 0.3 M caproic acid and 0.6M MOPS, an elution buffer comprising 10 mM Tris with 5.6 mM HCl, a highconcentration of elution buffer for buffering) in each of the channels.A sample comprising 50,000 immortalized human cells lysed using themethods described herein was prepared and loaded into each of thechannels. A pre-elution isotachophoresis separation was performed bydriving 900 pA per channel through the channel for 1900 seconds. After1900 seconds 3001, the current was reduced and 250 pA was applied toeach channel to drive the nucleic acids into the elution reservoir. 100seconds after starting isotachophoresis, signal processing using thevoltage on the driving electrode as the data source was started 3002.The top line shown represents the voltage and the bottom line representsthe derivative of the voltage. Two triggers were used to change thedriving current (corresponding to triggers 1 and 4 described in FIG. 16,at locations C and D, respectively). Low-conductivity ions (e.g. sampleions or trailing electrolytes) entering the elution reservoir or channelcan be detected by monitoring for peaks or maximums in the derivative ofthe voltage. The current was turned on at a first trigger point(trigger 1) 3001 to direct nucleic acids into the channel comprisingelution buffer and signal processing 3002 was started shortlythereafter. A first increase was detected at trigger point 3 3003 as thenucleic acids entered the elution reservoir and a second increase wasdetected at trigger point 4 3004 as the trailing electrolytes began toenter the elution reservoir. The current was removed following detectionof the second increase at trigger point 4 3004 so as to position orisolate the sample nucleic acids in the elution well.

Example 13—Temperature Sensing and End-of-Run Triggering

FIG. 21 shows exemplary temperature measurement results using aninfra-red thermal sensor to trigger a reduction or elimination of anelectric current in one of the channels. A fluidic device comprising 8channels was loaded with ITP buffers (leading electrolyte buffercomprising 88 mM Tris with 44 mM HCl, a high concentration of leadingelectrolyte for buffering, trailing electrolyte buffer comprising 1.2 MTris with 0.3 M caproic acid and 0.6 M MOPS, an elution buffercomprising 10 mM Tris with 5.6 mM HCl, a high concentration of elutionbuffer for buffering) in each of the channels. A sample comprising50,000 immortalized human cells lysed using the methods described hereinwas prepared and loaded into each of the channels. A pre-elutionisotachophoresis separation was performed by driving 900 ρA per channelthrough the channel for 1900 seconds. After 1900 seconds, the currentwas reduced and 250 ρA was applied to each channel to drive the nucleicacids into the elution reservoir. 100 seconds after startingisotachophoresis, signal processing using temperature data collected bya TMP007 infrared temperature sensor. The temperature was detected atlocation 2105 in the elution channel near the elution reservoir 2106,centered approximately 4.5 mm from the elution well 2106. Thetemperature sensor was place approximately 1 mm to 3 mm below the bottomsurface of the fluidic channel. The temperature sensor may be centeredapproximately 4.5 mm from the elution reservoir 2106 (with edges atabout 3.55 mm to about 5.45 mm from the elution reservoir). Thetemperature sensor was configured to detect temperature changes due toelectrophoretic Joule heating in the channel. Electrophoretic joule heatdissipation per channel volume may be inversely proportional toconductivity at a constant current. During isotachophoresis,lower-conductivity ions (trailing electrolytes) may displace higherconductivity ions (leading electrolytes) as the ITP zone moves throughthe channel. The temperature sensor may sense the ITP zone moving pastthe detection location 2105, and the displacement of ions as the ITPzone moves, as a rise in temperature within the channel at the detectionlocation.

The top line shows the temperature at the detection location 2105 andthe bottom line shows the derivative of the temperature. The temperaturewas monitored in real-time for high derivatives in order to detectlower-conductivity buffer zones. The vertical lines indicate when keyevents occurred during monitoring. From left to right, the first line2101 indicates the time at which the current was turned on and thesecond line 2102 indicates the start of signal processing shortlythereafter. The third line 2103 indicates the first detection of anincrease in the derivative of the temperature, and the fourth line 2104indicates the second detection of an increase in the derivative of thetemperature, at which point the current was stopped and the voltage wasdisabled so as to land the voltage in the reservoir and position orisolate the nucleic acids in the elution reservoir.

Example 14—Simultaneous ITP in an 8-Channel Fluidic Device

FIG. 31A, FIG. 31B, FIG. 31C, and FIG. 31D show the results ofsimultaneously performing isotachophoresis in 8 channels of a fluidicdevice. DNA was extracted from cell culture lysate using a bench topcontroller device to automate isotachophoresis in a monolithic,8-channel fluidic device. Leading electrolyte buffer containing 88 mMTris with 44 mM HCl and 0.002% Tween 20 was loaded into the leadingelectrolyte reservoir of each channel. Trailing electrolyte comprising1.2M Tris with 0.3 M Caproic Acid and 0.6 M MOPS with 0.002% Tween 20was loaded into the trailing electrolyte reservoir of each channel. Thesample for each channel was prepared in a second leading electrolytebuffer (e.g. sample buffer) comprising 10 mM Tris with 5.6 mM HCl with0.002% Tween 20. Each sample comprised a cell lysate. The total numberof human COLO 320 cells per sample represented 100,000 diploid genomeequivalents. Cells were pelleted and lysed off-chip in a lysis solutioncomprising 40 mM NaOH for 2 minutes and subsequently quenched at a 1:1volume ratio with a buffered acidic solution to bring the final celllysate sample to 10 mM Tris with 5.6 mM HCl and 20 mM NaCl at pH 8.Proteinase K was added to a final concentration of 400 μg/ml within thecell lysate sample volume. Four of the eight samples were treated withRNase A at a final concentration of 200 μg/ml and allowed to stand atroom temperature for 2 minutes. All eight samples were then incubatedfor 10 minutes at 56° C. The lysed samples were then brought to roomtemperature and loaded into the separate eight samplereservoirs/channels on the microfluidic device, denoted by channels Athrough H, in preparation for isotachophoresis. The four samples thatwere not treated with RNase A were loaded into channels B, D, F and H.The four samples treated with RNase A were loaded into channels A, C, E,and G. Samples treated with RNase A contained additional buffering ionsto enable optimal RNase activity, and therefore represented higher ionicstrength or higher conductivity samples that, under fixed current (ITPconditions), resulted in different voltage data traces than the samplesnot treated with RNase. The independent electrical circuit control ofchannels A through H enabled voltage signal and feedback control forautomated control and end-run triggering for each of the differentchannels of the device. FIG. 31A shows a micrograph of ITP bands withfocused DNA 3101 in each of the 8 samples in the sample channel regionof the device. The ITP band of DNA 3101 migrates within the channel inresponse to an applied electric field. The ITP band first travels awayfrom the trailing electrolyte reservoir in the direction indicated byarrow 3102. The ITP band 3101 then traverses the 180° low-dispersionturn and continues through the channel towards the elution reservoir inthe opposite direction (with respect to the chip) 3103 in response tothe applied electric field. FIG. 31B shows independent voltage signaldata at fixed currents for each of the 8 channels over time. FIG. 31Cshows a micrograph of the same 8 ITP bands with focused DNA 3101 fromthe samples eluted in the elution reservoir by independently controlledend-of-run voltage based triggering (this image represents the end ofthe run with the electrical field automatically shut off). FIG. 31D is amagnified section of the voltage tracing (monitoring) used fortriggering shown in FIG. 31B. The electric current of each channel wasindependently applied to the channel and the voltage of each channel wasindependently monitored in order to trigger a change (in this casecessation) in the electric field applied to each channel independentlyof every other channel.

As used herein, the term “or” means “and/or” unless stated otherwise.

The term “about” as used herein, unless otherwise indicated, refers to avalue that is no more than 10% above or below the value being modifiedby the term. For example, the term “about −20° C.” means a range of from−22° C. to −18° C. As another example, “about 1 hour” means a range offrom 54 minutes to 66 minutes.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It can be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

1. A method for sample purification, comprising: (a) loading into afluidic device (i) a tissue sample comprising lysed solid tissue,wherein said lysed solid tissue comprises nucleic acids and acontaminant, (ii) a trailing electrolyte buffer comprising firsttrailing electrolyte ions with an effective mobility having a magnitudelower than a magnitude of an effective mobility of said nucleic acids,and (iii) a leading electrolyte buffer comprising first leadingelectrolyte ions, with a second effective mobility, wherein said secondeffective mobility has a magnitude greater than said magnitude of saideffective mobility of said nucleic acids; and (b) applying an electricfield within said fluidic device to conduct isotachophoresis with saidfirst trailing electrolyte ions, said nucleic acids, and said firstleading electrolyte ions, thereby purifying said nucleic acids from saidcontaminant in said tissue sample.
 2. The method of claim 1, whereinsaid effective mobility of said first trailing electrolyte ions has amagnitude greater than a magnitude of an effective mobility of saidcontaminant.
 3. (canceled)
 4. The method of claim 1, further comprisingin a first zone of said microfluidic chip, conducting on said tissuesample at least one sample preparation procedure selected from the groupconsisting of (1) removing embedding material, (2) disrupting tissue,(3) lysing cells, (4) de-crosslinking said nucleic acids, (5) digestingproteins, and (6) digesting said nucleic acids.
 5. The method of claim4, wherein said isotachophoresis is conducted in a second zone of saidmicrofluidic chip, wherein said second zone is separate from andfluidically connected to said first zone.
 6. (canceled)
 7. The method ofclaim 1, wherein said lysed solid tissue comprises a chemical fixative.8.-11. (canceled)
 12. The method of claim 1, wherein said lysed solidtissue comprises solid particles.
 13. (canceled)
 14. The method of claim1, wherein said contaminant is selected from the group consisting ofcrosslinked nucleic acids, embedding material, paraffin, tissue debris,fixation chemicals, formalin, proteins, inhibitors, and combinationsthereof. 15.-29. (canceled)
 30. The method of claim 4, wherein saidsample preparation procedure comprises disrupting tissue or lysing cellsby applying a solution comprising urea to said tissue or cell sample.31. The method of claim 30, wherein said solution further comprisesthiourea. 32.-35. (canceled)
 36. The method of claim 1, furthercomprising eluting an output solution comprising said purified nucleicacids from an outlet reservoir of said fluidic device.
 37. The method ofclaim 36, wherein a concentration of said purified nucleic acids in saidoutput solution is at least about two-fold higher than a concentrationof said nucleic acids in said tissue sample. 38.-39. (canceled)
 40. Themethod of claim 1, wherein said first trailing electrolyte ions comprisecaproic acid or wherein said first leading electrolyte ions comprisechloride.
 41. (canceled)
 42. The method of claim 1, wherein saidtrailing electrolyte buffer comprises second trailing electrolyte ionshaving a different effective mobility than said first trailingelectrolyte ions.
 43. The method of claim 42, wherein said secondtrailing electrolyte ions comprise HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) or MOPS(3-(N-morpholino)propanesulfonic acid) and wherein said first trailingelectrolyte ions comprise caproic acid. 44.-45. (canceled)
 46. Themethod of claim 42, wherein said second trailing electrolyte ionscomprise HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) andsaid first trailing electrolyte ions comprise MOPS. 47.-52. (canceled)53. A method for simultaneously purifying nucleic acids from at leasttwo different samples comprising: (a) loading into a first channel of amicrofluidic chip (i) a first sample comprising first nucleic acids anda first contaminant, (ii) a first trailing electrolyte buffer comprisingfirst trailing ions, wherein a magnitude of an effective mobility ofsaid first trailing ions is less than a magnitude of an effectivemobility of said first nucleic acids, and (iii) a first leadingelectrolyte buffer comprising first leading ions, wherein a magnitude ofan effective mobility of said first leading ions is greater than saidmagnitude of said effective mobility of said first nucleic acids; (b)loading into a second channel of said microfluidic chip (i) a secondsample comprising second nucleic acids and a second contaminant, (ii) asecond trailing electrolyte buffer comprising second trailing ions,wherein a magnitude of said second trailing ions is less than amagnitude of an effective mobility of said second nucleic acids, and(iii) a second leading electrolyte buffer comprising second leadingions, wherein a magnitude of an effective mobility of said secondleading ions is greater than said magnitude of said effective mobilityof said second nucleic acids; and (c) applying a first electric fieldwithin said microfluidic chip to conduct isotachophoresis in said firstchannel with said first trailing ions, said first nucleic acids, andsaid first leading ions, and applying a second electric field to conductisotachophoresis in said second channel with said second trailing ions,said second nucleic acids, and said second leading ions, therebysimultaneously purifying said first nucleic acids from said firstcontaminant and said second nucleic acids from said second contaminant.54.-110. (canceled)
 111. A microfluidic device comprising: (a) a firstisotachophoresis region in a microfluidic chip comprising: (i) a firstsample reservoir in fluid communication with a first fluidic channel,(ii) a first buffer reservoir in fluid communication with said firstfluidic channel, and (iii) a second buffer reservoir in fluidcommunication with said first channel; and (b) a second isotachophoresisregion in said microfluidic chip comprising: (i) a second samplereservoir in fluid communication with a second fluidic channel, (ii) athird buffer reservoir in fluid communication with said second fluidicchannel, and (iii) a fourth buffer reservoir in fluid communication withsaid second channel, wherein said first isotachophoresis region is notin fluid communication with said second isotachophoresis region andwherein said microfluidic device is configured to independently controla first electric circuit that applies current to said firstisotachophoresis region and a second electric circuit that appliescurrent to said second isotachophoresis region. 112.-150. (canceled)151. A microfluidic system, said microfluidic system comprising: (a) amicrofluidic chip comprising a first channel and a first reservoir influid communication with said first channel, wherein said first channeland said first reservoir meet at a first junction; and (b) a mechanicalmember comprising a first tooth, wherein said mechanical member isconfigured to apply mechanical pressure to said first channel via saidfirst tooth in order to at least partially close said first channel byplastic deformation of at least one wall of said first channel andincrease fluid resistance between said first channel and said firstreservoir. 152.-161. (canceled)
 162. A method of performingisotachophoresis on a sample comprising nucleic acids comprising: (a)loading said sample comprising nucleic acids into a first reservoir of amicrofluidic chip; (b) loading a trailing electrolyte buffer into asecond reservoir of said microfluidic chip, wherein said trailingelectrolyte buffer comprises first trailing electrolyte ions with aneffective mobility having a magnitude lower than a magnitude of aneffective mobility of said nucleic acids; (c) loading a leadingelectrolyte buffer into a third reservoir of said microfluidic chip,wherein said third reservoir comprises first leading electrolyte ionswith a second effective mobility, wherein said second effective mobilityhas a magnitude greater than said magnitude of said effective mobilityof said nucleic acids; (d) applying an electric field within saidmicrofluidic chip to conduct isotachophoresis with said first trailingelectrolyte ions, said nucleic acids, and said first leading electrolyteions, thereby confining said nucleic acids, or a portion thereof, to anisotachophoresis zone; and (e) using a temperature sensor to sense atemperature change in or near said isotachophoresis zone, whereinfeedback from said temperature sensor is used to control said electricfield. 163.-166. (canceled)
 167. A microfluidic device comprising: (a) afirst isotachophoresis region in a microfluidic chip comprising: (i) afirst sample reservoir in fluid communication with a first fluidicchannel; (ii) a first, a second, and a third buffer reservoir in fluidcommunication with said first fluidic channel, wherein said first andsecond buffer reservoirs are separated by a capillary barrier; and (iii)an elution reservoir in fluid communication with said first fluidicchannel; (b) a sensor configured to detect a temperature change in saidfirst fluidic channel within said first isotachophoresis region; and (c)an apparatus positioned to supply electrical current within said firstchannel within said first isotachophoresis region. 168.-179. (canceled)